# gene_set_details

description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6877
exact_source: GSE4590_3554_200_UP
source_species_code: HS
GEO_id: GSE4590
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated during B lymphocyte differentiation: large pre-B II versus VPREB1+ [GeneID=7441] pre-B Il.


description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6878
exact_source: GSE4590_3554_200_DN
source_species_code: HS
GEO_id: GSE4590
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated during B lymphocyte differentiation: large pre-B II versus VPREB1+ [GeneID=7441] pre-B Il.


systematic_name: M6880
exact_source: GSE9601_3810_200_UP
source_species_code: HS
GEO_id: GSE9601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes after HCMV infection: untreated versus BAY 11-7082 [PubChem=5353431].

description_full:
  Human cytomegalovirus induces a pro-inflammatory monocyte following infection and we have evidence that NF-κB and phosphatidylinositol 3-kinase [PI(3)K] are key mediators in this early activation. To begin to address how these signalling pathways are responsible for the rapid activation of infected monocytes, we examined the role these pathways played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes, including inflammatory genes, were regulated in a NF-κB- and/or PI(3)K-dependent manner, identifying these pathways as key cellular control points in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.


systematic_name: M6881
exact_source: GSE9601_3810_200_DN
source_species_code: HS
GEO_id: GSE9601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes after HCMV infection: untreated versus BAY 11-7082 [PubChem=5353431].

description_full:
  Human cytomegalovirus induces a pro-inflammatory monocyte following infection and we have evidence that NF-κB and phosphatidylinositol 3-kinase [PI(3)K] are key mediators in this early activation. To begin to address how these signalling pathways are responsible for the rapid activation of infected monocytes, we examined the role these pathways played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes, including inflammatory genes, were regulated in a NF-κB- and/or PI(3)K-dependent manner, identifying these pathways as key cellular control points in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.


systematic_name: M6884
exact_source: GSE9601_3812_200_UP
source_species_code: HS
GEO_id: GSE9601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes after HCMV infection: BAY 11-7082 [PubChem=5353431] versus Ly294002 [PubChem=3973].

description_full:
[cell repeats an earlier one in this file: 736 characters]


systematic_name: M6887
exact_source: GSE9601_3812_200_DN
source_species_code: HS
GEO_id: GSE9601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes after HCMV infection: BAY 11-7082 [PubChem=5353431] versus Ly294002 [PubChem=3973].

description_full:
[cell repeats an earlier one in this file: 736 characters]


systematic_name: M6888
exact_source: GSE9316_2840_200_UP
source_species_code: MM
GEO_id: GSE9316
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with in vivo expansion: IL6 [GeneID=3569] versus IFNG [GeneID=3458].

description_full:
  Th17 cells are enriched by sorting FR4-CD4+ T cells from SKG mice. A large number of Th17 cells also develop spontaneously when CD4+ T cells from IFN-g-deficient (IFN-g-/-) BALB/c mice are transferred to T cell-deficient RAG2-deficient (RAG2-/-) mice and subjected to homeostatic proliferation, whereas they fail to develop in similar transfer of IL-6-deficient (IL-6-/-) CD4+ T cells to IL-6-/- RAG2-/- mice. To explore the functional molecules specifically expressed by Th17 cells, we conducted Gene Microarray analysis between 10-month-old SKG FR4-CD4+ cells and age-matched BALB/c FR4-CD4+ cells, and between IFN-g-/- CD4+ cells transferred to RAG2-/- mice and IL-6-/- CD4+ T cells transferred to IL-6-/- RAG2-/- mice. The analysis revealed that 1,556 and 115 genes were up-regulated in 10-month-old SKG FR4-CD4+ and IFN-g-/- CD4+ T cells after homeostatic proliferation, respectively, with 29 genes shared by the two groups of genes. The 29 genes included those encoding cytokines, chemokines, and their receptors, such as IL-1 receptor type1 (IL-1R1), IL-17, IL-22, IL-21, CCR6, and CCL20.


systematic_name: M6892
exact_source: GSE9316_2840_200_DN
source_species_code: MM
GEO_id: GSE9316
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with in vivo expansion: IL6 [GeneID=3569] versus IFNG [GeneID=3458].

description_full:
  Th17 cells are enriched by sorting FR4-CD4+ T cells from SKG mice. A large number of Th17 cells also develop spontaneously when CD4+ T cells from IFN-g-deficient (IFN-g-/-) BALB/c mice are transferred to T cell-deficient RAG2-deficient (RAG2-/-) mice and subjected to homeostatic proliferation, whereas they fail to develop in similar transfer of IL-6-deficient (IL-6-/-) CD4+ T cells to IL-6-/- RAG2-/- mice. To explore the functional molecules specifically expressed by Th17 cells, we conducted Gene Microarray analysis between 10-month-old SKG FR4-CD4+ cells and age-matched BALB/c FR4-CD4+ cells, and between IFN-g-/- CD4+ cells transferred to RAG2-/- mice and IL-6-/- CD4+ T cells transferred to IL-6-/- RAG2-/- mice. The analysis revealed that 1,556 and 115 genes were up-regulated in 10-month-old SKG FR4-CD4+ and IFN-g-/- CD4+ T cells after homeostatic proliferation, respectively, with 29 genes shared by the two groups of genes. The 29 genes included those encoding cytokines, chemokines, and their receptors, such as IL-1 receptor type1 (IL-1R1), IL-17, IL-22, IL-21, CCR6, and CCL20.


systematic_name: M6893
exact_source: GSE9316_2841_200_UP
source_species_code: MM
GEO_id: GSE9316
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in FOLR4- CD4 [GeneID=390243;920] T cells treated by phorbol myristate acetate and ionomycin [PubChem=4792;3733] from: BALB/c versus SKG mice.

description_full:
  Th17 cells are enriched by sorting FR4-CD4+ T cells from SKG mice. A large number of Th17 cells also develop spontaneously when CD4+ T cells from IFN-g-deficient (IFN-g-/-) BALB/c mice are transferred to T cell-deficient RAG2-deficient (RAG2-/-) mice and subjected to homeostatic proliferation, whereas they fail to develop in similar transfer of IL-6-deficient (IL-6-/-) CD4+ T cells to IL-6-/- RAG2-/- mice. To explore the functional molecules specifically expressed by Th17 cells, we conducted Gene Microarray analysis between 10-month-old SKG FR4-CD4+ cells and age-matched BALB/c FR4-CD4+ cells, and between IFN-g-/- CD4+ cells transferred to RAG2-/- mice and IL-6-/- CD4+ T cells transferred to IL-6-/- RAG2-/- mice. The analysis revealed that 1,556 and 115 genes were up-regulated in 10-month-old SKG FR4-CD4+ and IFN-g-/- CD4+ T cells after homeostatic proliferation, respectively, with 29 genes shared by the two groups of genes. The 29 genes included those encoding cytokines, chemokines, and their receptors, such as IL-1 receptor type1 (IL-1R1), IL-17, IL-22, IL-21, CCR6, and CCL20.


systematic_name: M6894
exact_source: GSE9316_2841_200_DN
source_species_code: MM
GEO_id: GSE9316
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in FOLR4- CD4 [GeneID=390243;920] T cells treated by phorbol myristate acetate and ionomycin [PubChem=4792;3733] from: BALB/c versus SKG mice.

description_full:
[cell repeats an earlier one in this file: 1095 characters]


systematic_name: M6895
exact_source: GSE9509_3052_200_UP
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 10 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
  IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes.


systematic_name: M6896
exact_source: GSE9509_3052_200_DN
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 10 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
  IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes.


systematic_name: M6899
exact_source: GSE9509_3053_200_UP
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 20 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
  IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes.


systematic_name: M6901
exact_source: GSE9509_3053_200_DN
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 20 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6902
exact_source: GSE9509_3054_200_UP
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 30 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6903
exact_source: GSE9509_3054_200_DN
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with IL10 [GeneID=3586] knockout in response to 30 min treatment by: LPS versus LPS and IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6904
exact_source: GSE9509_3055_200_UP
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with IL10 [GeneID=3586] knockout treated by LPS: 10 min versus 30 min.

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6908
exact_source: GSE9509_3055_200_DN
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with IL10 [GeneID=3586] knockout treated by LPS: 10 min versus 30 min.

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6909
exact_source: GSE9509_3056_200_UP
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with IL10 [GeneID=3586] knockout treated by LPS and IL10 [GeneID=3586]: 10 min versus 30 min.

description_full:
[cell repeats an earlier one in this file: 1177 characters]


systematic_name: M6911
exact_source: GSE9509_3056_200_DN
source_species_code: MM
GEO_id: GSE9509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with IL10 [GeneID=3586] knockout treated by LPS and IL10 [GeneID=3586]: 10 min versus 30 min.

description_full:
[cell repeats an earlier one in this file: 1177 characters]


description_brief: Genes up-regulated in B lymphocytes: control versus anti IgM.
systematic_name: M6915
exact_source: GSE6674_3086_200_UP
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  We have previously shown that rheumatoid factors (RF) produced by Fas-deficient autoimmune-prone mice typically bind autologous IgG2a with remarkably low affinity. Nevertheless, B cells representative of this RF population proliferate vigorously in response IgG2a/chromatin immune complexes through a mechanism dependent on the sequential engagement of the BCR and Toll-like receptor 9 (TLR9). To more precisely address the role of both receptors in this response, we analyzed the signaling pathways activated in AM14 B cells stimulated with these complexes. We found that the BCR not only serves to direct the chromatin complex to an internal compartment where it can engage TLR9 but also transmits a suboptimal signal that in combination with the signals emanating from TLR9 leads to NF-kappa-B activation and proliferation. Importantly, engagement of both receptors leads to the upregulation of a group of gene products, not induced by the BCR or TLR9 alone, that include IL-2. These data indicate that autoreactive B cells, stimulated by a combination of BCR and TLR9 ligands, acquire functional properties that may contribute to the activation of additional cells involved in the autoimmune disease process.


systematic_name: M6926
exact_source: GSE6674_3089_200_DN
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes: control versus anti IgM and cell anti IgM and CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 1212 characters]


systematic_name: M6940
exact_source: GSE6674_3094_200_UP
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes: CpG oligodeoxynucleotide 1826 versus anti IgM and CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 1212 characters]


systematic_name: M6941
exact_source: GSE6674_3094_200_DN
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes: CpG oligodeoxynucleotide 1826 versus anti IgM and CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 1212 characters]


systematic_name: M6942
exact_source: GSE6674_3095_200_UP
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes: PL2-3 (Chromatin IC) versus anti IgM and CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 1212 characters]


systematic_name: M6943
exact_source: GSE6674_3095_200_DN
source_species_code: MM
GEO_id: GSE6674
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes: PL2-3 (Chromatin IC) versus anti IgM and CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 1212 characters]


systematic_name: M6944
exact_source: GSE7831_3531_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoit dendritic cells (1h): untreated versus CpG oligodeoxynucleotide 1826.

description_full:
  CpG 1826 binds to Toll-like receptor (TLR)9, whereas influenza virus PR8 activates pDC via TLR7. Differential stimulation of pDCs is expected to result in unique activation mechanism(s) leading to a different phenotypically and functionally matured pDC We used microarrays to detail the global programme of gene expression underlying the maturation process of pDC activated with CpG 1826 and influenza virus PR8. We identified a distinct expression profile of upregulated immunomediators.


systematic_name: M6945
exact_source: GSE7831_3531_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoit dendritic cells (1h): untreated versus CpG oligodeoxynucleotide 1826.

description_full:
  CpG 1826 binds to Toll-like receptor (TLR)9, whereas influenza virus PR8 activates pDC via TLR7. Differential stimulation of pDCs is expected to result in unique activation mechanism(s) leading to a different phenotypically and functionally matured pDC We used microarrays to detail the global programme of gene expression underlying the maturation process of pDC activated with CpG 1826 and influenza virus PR8. We identified a distinct expression profile of upregulated immunomediators.


systematic_name: M6947
exact_source: GSE7831_3532_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (1h): untreated versus influenza virus infection.

description_full:
  CpG 1826 binds to Toll-like receptor (TLR)9, whereas influenza virus PR8 activates pDC via TLR7. Differential stimulation of pDCs is expected to result in unique activation mechanism(s) leading to a different phenotypically and functionally matured pDC We used microarrays to detail the global programme of gene expression underlying the maturation process of pDC activated with CpG 1826 and influenza virus PR8. We identified a distinct expression profile of upregulated immunomediators.


systematic_name: M6949
exact_source: GSE7831_3532_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (1h): untreated versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6950
exact_source: GSE7831_3533_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (1h): CpG oligodeoxynucleotide 1826 versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6952
exact_source: GSE7831_3533_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (1h): CpG oligodeoxynucleotide 1826 versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6953
exact_source: GSE7831_3534_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoit dendritic cells (4h): untreated versus CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6954
exact_source: GSE7831_3534_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoit dendritic cells (4h): untreated versus CpG oligodeoxynucleotide 1826.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6955
exact_source: GSE7831_3535_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (4h): untreated versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6956
exact_source: GSE7831_3535_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (4h): untreated versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6958
exact_source: GSE7831_3536_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (4h): CpG oligodeoxynucleotide 1826 versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6959
exact_source: GSE7831_3536_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (4h): CpG oligodeoxynucleotide 1826 versus influenza virus infection.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6960
exact_source: GSE7831_3537_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells in response to CpG oligodeoxynucleotide 1826: 1h versus 4h.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6961
exact_source: GSE7831_3537_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells in response to CpG oligodeoxynucleotide 1826: 1h versus 4h.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6963
exact_source: GSE7831_3538_200_UP
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells in response to influenza virus infection: 1h versus 4h.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6964
exact_source: GSE7831_3538_200_DN
source_species_code: MM
GEO_id: GSE7831
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells in response to influenza virus infection: 1h versus 4h.

description_full:
[cell repeats an earlier one in this file: 488 characters]


systematic_name: M6965
exact_source: GSE9239_2477_200_UP
source_species_code: HS
GEO_id: GSE9239
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: control versus TNF [GeneID=7124] inhibitor etanercept.

description_full:
  The process for making monocyte derived DCs (moDCs) has been previously described (46). All analysis was performed on “day 5” immature DCs. Etanercept 10mg/mL was added to experimental wells on days 0, 2, and 4. We chose this concentration of etanercept as it approximates the plasma concentration of drug when given 50mg BIW.


systematic_name: M6966
exact_source: GSE9239_2477_200_DN
source_species_code: HS
GEO_id: GSE9239
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: control versus TNF [GeneID=7124] inhibitor etanercept.

description_full:
  The process for making monocyte derived DCs (moDCs) has been previously described (46). All analysis was performed on “day 5” immature DCs. Etanercept 10mg/mL was added to experimental wells on days 0, 2, and 4. We chose this concentration of etanercept as it approximates the plasma concentration of drug when given 50mg BIW.


description_brief: Genes up-regulated in naïve macrophages: untreated versus LPS.
systematic_name: M6970
exact_source: GSE8621_3518_200_UP
source_species_code: MM
GEO_id: GSE8621
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Among the multiple mechanisms that control the intensity and duration of macrophage activation, the development of a state of refractoriness to a second stimulation in cells treated with LPS has long been recognized. Release of inhibitory cytokines and alterations in intracellular signaling pathways may be involved in the development of LPS tolerance. Although a number of molecules have been implicated, a detailed picture of the molecular changes in LPS tolerance is still missing. We have used a genome-wide gene expression analysis approach to (i) define which fraction of LPS target genes are subject to tolerance induction and (ii) identify genes that are expressed at high levels in tolerant macrophages. Our data show that in LPS tolerant macrophages the vast majority of LPS-induced gene expression is abrogated. The extent of tolerance induction varies for individual genes, and a small subset appears to be excepted. Compared to other negative control mechanisms of macrophages, e.g. IL-10-induced deactivation, LPS-tolerance inhibits a much wider range of transcriptional targets. Some previously described negative regulators of TLR-signaling (e.g. IRAK-M) were confirmed as expressed at higher levels in LPS-tolerant macrophages. In addition, we discuss other potential players in LPS tolerance identified in this group of genes.


systematic_name: M6988
exact_source: GSE9878_2935_200_UP
source_species_code: MM
GEO_id: GSE9878
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in pro-B cells with PAX5 [GeneID=5079] knockout: control versus over-expressing EBF1 [GeneID=1879].

description_full:
  We have determined that sustained expression of EBF suppresses alternate lineage genes independently of Pax5.


systematic_name: M6989
exact_source: GSE9878_2935_200_DN
source_species_code: MM
GEO_id: GSE9878
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in pro-B cells with PAX5 [GeneID=5079] knockout: control versus over-expressing EBF1 [GeneID=1879].

description_full:
  We have determined that sustained expression of EBF suppresses alternate lineage genes independently of Pax5.


systematic_name: M6990
exact_source: GSE5503_3156_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus mesenteric lymph nodes (mLN).

description_full:
  Transcriptional response of murine allogeneic T cells (B10.BR) after stimulation with different organ-derived (spleen, liver, peripheral and mesenteric lymph nodes) dendritic cells (C57BL/6) in vitro


systematic_name: M6991
exact_source: GSE5503_3156_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus mesenteric lymph nodes (mLN).

description_full:
  Transcriptional response of murine allogeneic T cells (B10.BR) after stimulation with different organ-derived (spleen, liver, peripheral and mesenteric lymph nodes) dendritic cells (C57BL/6) in vitro


systematic_name: M6992
exact_source: GSE5503_3157_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus peripheral lymph nodes (pLN).

description_full:
  Transcriptional response of murine allogeneic T cells (B10.BR) after stimulation with different organ-derived (spleen, liver, peripheral and mesenteric lymph nodes) dendritic cells (C57BL/6) in vitro


systematic_name: M6993
exact_source: GSE5503_3157_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus peripheral lymph nodes (pLN).

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M6996
exact_source: GSE5503_3158_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M6997
exact_source: GSE5503_3158_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from: liver versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M7000
exact_source: GSE5503_3159_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from lymph nodes: mesenteric (mLN) versus peripheral (pLN).

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M291
exact_source: GSE5503_3159_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from lymph nodes: mesenteric (mLN) versus peripheral (pLN).

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M293
exact_source: GSE5503_3160_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from: mesenteric lymph nodes (mLN) versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M294
exact_source: GSE5503_3160_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from: mesenteric lymph nodes (mLN) versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M296
exact_source: GSE5503_3161_200_UP
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in allogeneic T cells after stimulation with dendritic cells from: peripheral lymph nodes (mLN) versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M297
exact_source: GSE5503_3161_200_DN
source_species_code: MM
GEO_id: GSE5503
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in allogeneic T cells after stimulation with dendritic cells from: peripheral lymph nodes (mLN) versus spleen.

description_full:
[cell repeats an earlier one in this file: 199 characters]


systematic_name: M298
exact_source: GSE10240_2953_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells: control versus stimulated with IL17A [GeneID=3605].

description_full:
  Primary HBE cells were stimulated with IL-22 and IL-17, and gene expression was studied using an Affymetrix platform microarray, in order to investigate which genes may be upregulated or downregulated in response to these cytokines. Of particular interest was the host defense genes such as antimicrobial peptides, which have been shown to be upregulated by IL-22 and IL-17 in skin keratinocytes.


systematic_name: M299
exact_source: GSE10240_2955_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells stimulated with: IL22 [GeneID=50616] versus IL17A [GeneID=3605].

description_full:
  Primary HBE cells were stimulated with IL-22 and IL-17, and gene expression was studied using an Affymetrix platform microarray, in order to investigate which genes may be upregulated or downregulated in response to these cytokines. Of particular interest was the host defense genes such as antimicrobial peptides, which have been shown to be upregulated by IL-22 and IL-17 in skin keratinocytes.


systematic_name: M300
exact_source: GSE10240_2953_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells: control versus stimulated with IL17A [GeneID=3605].

description_full:
  Primary HBE cells were stimulated with IL-22 and IL-17, and gene expression was studied using an Affymetrix platform microarray, in order to investigate which genes may be upregulated or downregulated in response to these cytokines. Of particular interest was the host defense genes such as antimicrobial peptides, which have been shown to be upregulated by IL-22 and IL-17 in skin keratinocytes.


systematic_name: M301
exact_source: GSE10240_2952_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells: control versus stimulated with IL22 [GeneID=50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M302
exact_source: GSE10240_2952_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells: control versus stimulated with IL22 [GeneID=50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M303
exact_source: GSE10240_2954_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells: control versus stimulated with IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M304
exact_source: GSE10240_2954_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells: control versus stimulated with IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M306
exact_source: GSE10240_2956_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells stimulated with: IL22 [GeneID=50616] versus IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M309
exact_source: GSE10240_2956_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells stimulated with: IL22 [GeneID=50616] versus IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M310
exact_source: GSE10240_2955_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells stimulated with: IL22 [GeneID=50616] versus IL17A [GeneID=3605].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M312
exact_source: GSE10240_2957_200_DN
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in primary bronchial epithelial cells stimulated with: IL17A [GeneID=50616] versus IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M313
exact_source: GSE10240_2957_200_UP
source_species_code: HS
GEO_id: GSE10240
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in primary bronchial epithelial cells stimulated with: IL17A [GeneID=50616] versus IL17A and IL22 [GeneID=3605;50616].

description_full:
[cell repeats an earlier one in this file: 396 characters]


systematic_name: M315
exact_source: GSE10273_2545_200_UP
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cells treated with 0.25 ng/ml IL7 [GeneID=3574] versus the cells treated with 5 ng/ml IL7 [GeneID=3574] and transduced with IRF4 [GeneID=3662].

description_full:
  Productive rearrangement of the immunoglobulin heavy chain locus triggers a major developmental checkpoint that promotes limited clonal expansion of pre-B cells, culminating in cell cycle arrest and rearrangement of the kappa (κ) or lambda (λ) light-chain loci. B lineage cells lacking the related transcription factors IRF-4 and IRF-8 undergo a developmental arrest at the cycling pre-B cell stage and are blocked for light-chain recombination. Using Irf-4,8-/- pre-B cells we demonstrate that two pathways converge to synergistically drive light-chain rearrangement, a process that is not simply activated by cell cycle exit. One pathway is directly dependent on IRF-4, whose expression is elevated by pre-BCR signaling. IRF-4 targets the κ 3′ and λ enhancers to increase locus accessibility and positions a kappa allele away from pericentromeric heterochromatin. The other pathway is triggered by attenuation of IL-7 signaling and results in activation of the κ intronic enhancer via binding of the transcription factor, E2A. Intriguingly, IRF-4 regulates the expression of CXCR4 and promotes the migration of pre-B cells in response to the chemokine CXCL12. We propose that IRF-4 coordinates the two pathways regulating light-chain recombination by positioning pre-B cells away from IL-7 expressing stromal cells. We used microarrys to identify the changes in gene expression under different levels of the cytokine IL-7 and after rescue of genetic defect.


systematic_name: M316
exact_source: GSE10273_2543_200_DN
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cells treated with IL7 [GeneID=3574]: 5 ng/ml versus 0.25ng/ml.

description_full:
  Productive rearrangement of the immunoglobulin heavy chain locus triggers a major developmental checkpoint that promotes limited clonal expansion of pre-B cells, culminating in cell cycle arrest and rearrangement of the kappa (κ) or lambda (λ) light-chain loci. B lineage cells lacking the related transcription factors IRF-4 and IRF-8 undergo a developmental arrest at the cycling pre-B cell stage and are blocked for light-chain recombination. Using Irf-4,8-/- pre-B cells we demonstrate that two pathways converge to synergistically drive light-chain rearrangement, a process that is not simply activated by cell cycle exit. One pathway is directly dependent on IRF-4, whose expression is elevated by pre-BCR signaling. IRF-4 targets the κ 3′ and λ enhancers to increase locus accessibility and positions a kappa allele away from pericentromeric heterochromatin. The other pathway is triggered by attenuation of IL-7 signaling and results in activation of the κ intronic enhancer via binding of the transcription factor, E2A. Intriguingly, IRF-4 regulates the expression of CXCR4 and promotes the migration of pre-B cells in response to the chemokine CXCL12. We propose that IRF-4 coordinates the two pathways regulating light-chain recombination by positioning pre-B cells away from IL-7 expressing stromal cells. We used microarrys to identify the changes in gene expression under different levels of the cytokine IL-7 and after rescue of genetic defect.


systematic_name: M317
exact_source: GSE10273_2544_200_DN
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cell treated with 5ng/ml IL7 [GeneID=3574] versus those transduced with IRF4 [GeneID=3662].

description_full:
  Productive rearrangement of the immunoglobulin heavy chain locus triggers a major developmental checkpoint that promotes limited clonal expansion of pre-B cells, culminating in cell cycle arrest and rearrangement of the kappa (κ) or lambda (λ) light-chain loci. B lineage cells lacking the related transcription factors IRF-4 and IRF-8 undergo a developmental arrest at the cycling pre-B cell stage and are blocked for light-chain recombination. Using Irf-4,8-/- pre-B cells we demonstrate that two pathways converge to synergistically drive light-chain rearrangement, a process that is not simply activated by cell cycle exit. One pathway is directly dependent on IRF-4, whose expression is elevated by pre-BCR signaling. IRF-4 targets the κ 3′ and λ enhancers to increase locus accessibility and positions a kappa allele away from pericentromeric heterochromatin. The other pathway is triggered by attenuation of IL-7 signaling and results in activation of the κ intronic enhancer via binding of the transcription factor, E2A. Intriguingly, IRF-4 regulates the expression of CXCR4 and promotes the migration of pre-B cells in response to the chemokine CXCL12. We propose that IRF-4 coordinates the two pathways regulating light-chain recombination by positioning pre-B cells away from IL-7 expressing stromal cells. We used microarrys to identify the changes in gene expression under different levels of the cytokine IL-7 and after rescue of genetic defect.


systematic_name: M318
exact_source: GSE10273_2543_200_UP
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cells treated with IL7 [GeneID=3574]: 5 ng/ml versus 0.25ng/ml.

description_full:
[cell repeats an earlier one in this file: 1459 characters]


systematic_name: M320
exact_source: GSE10273_2544_200_UP
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cell treated with 5ng/ml IL7 [GeneID=3574] versus those transduced with IRF4 [GeneID=3662].

description_full:
[cell repeats an earlier one in this file: 1459 characters]


systematic_name: M322
exact_source: GSE10273_2545_200_DN
source_species_code: MM
GEO_id: GSE10273
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IRF4 and IRF8 [GeneID=3662;3394] null pre-B cells treated with 0.25 ng/ml IL7 [GeneID=3574] versus the cells treated with 5 ng/ml IL7 [GeneID=3574] and transduced with IRF4 [GeneID=3662].

description_full:
[cell repeats an earlier one in this file: 1459 characters]


description_brief: Genes up-regulated in Sez-2 cells (T cell lymphoma): untreated versus IL2 [GeneID=3558].
systematic_name: M324
exact_source: GSE8685_3173_200_UP
source_species_code: HS
GEO_id: GSE8685
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  In this study we compared the effects of IL-2, IL-15, and IL-21 on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from the CD4+ cutaneous T-cell lymphoma (CTCL). Whereas both IL-2 and IL-15 that signal through receptors that share the common gamma chain and the beta chain modulated the expression of >1,000 genes, IL-21 that signals via the receptor also containing gamma chain up-regulated <40 genes. All three cytokines induced tyrosine phosphorylation of Jak1 and Jak3. However, only IL-2 and IL-15 strongly activated STAT5, PI3K/Akt, and MEK/ERK signaling pathways. In contrast, IL-21 selectively activated STAT3. Whereas all three cytokines protected CTCL cells from apoptosis, only IL-2 and IL-15 promoted their proliferation. The effects of the cytokine stimulation were Jak3- and Jak1-kinase dependent. These findings document the vastly different impact of IL-2 and IL-15 vs. IL-21 on malignant CD4+ T cells. They also suggest two novel therapeutic approaches to CTCL and, possibly, other CD4+ T cell lymphomas: inhibition of the Jak1/Jak3 kinase complex and, given the known strong immunostimulatory properties of IL-21 on CD8+ T, NK, and B cells, application of this cytokine to boost an immune response against malignant CD4+ T cells.


systematic_name: M335
exact_source: GSE8685_3177_200_DN
source_species_code: HS
GEO_id: GSE8685
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Sez-2 cells (T cell lymphoma): IL2 [GeneID=3558] versus IL21 [GeneID=59067].

description_full:
[cell repeats an earlier one in this file: 1303 characters]


systematic_name: M338
exact_source: GSE8685_3178_200_DN
source_species_code: HS
GEO_id: GSE8685
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Sez-2 cells (T cell lymphoma): IL15 [GeneID=3600] versus IL21 [GeneID=3600].

description_full:
[cell repeats an earlier one in this file: 1303 characters]


systematic_name: M339
exact_source: GSE7596_3419_200_UP
source_species_code: MM
GEO_id: GSE7596
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in T conv in response to TGF-beta: expressing constantly active form of AKT1 [GeneID=207] versus control.

description_full:
  The CD4+Foxp3+ regulatory T cells play an essential role in maintaining tolerance via their suppressive function on conventional T cells. The intracellular signaling pathways that regulate Foxp3 expression are largely unknown. In this study we describe a novel inhibitory role for AKT in regulating de novo induction of Foxp3 both in vivo and in vitro. A constitutively active allele of AKT significantly diminished TGF-â induced Foxp3 induction via a rapamycin-sensitive pathway, establishing a role for the AKT-mTOR axis in Treg cells. Moreover, the observed impairment in Foxp3 induction was paralleled by a selective downmodulation of the imparted Treg transcriptional signature highlighting the importance of the balance of intracellular signals in Treg differentiation . Our results provide a basis for further elucidation of molecular mechanisms that regulate Foxp3 induction and identify AKT as an important negative regulator of this process.


systematic_name: M340
exact_source: GSE7596_3419_200_DN
source_species_code: MM
GEO_id: GSE7596
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in T conv in response to TGF-beta: expressing constantly active form of AKT1 [GeneID=207] versus control.

description_full:
  The CD4+Foxp3+ regulatory T cells play an essential role in maintaining tolerance via their suppressive function on conventional T cells. The intracellular signaling pathways that regulate Foxp3 expression are largely unknown. In this study we describe a novel inhibitory role for AKT in regulating de novo induction of Foxp3 both in vivo and in vitro. A constitutively active allele of AKT significantly diminished TGF-â induced Foxp3 induction via a rapamycin-sensitive pathway, establishing a role for the AKT-mTOR axis in Treg cells. Moreover, the observed impairment in Foxp3 induction was paralleled by a selective downmodulation of the imparted Treg transcriptional signature highlighting the importance of the balance of intracellular signals in Treg differentiation . Our results provide a basis for further elucidation of molecular mechanisms that regulate Foxp3 induction and identify AKT as an important negative regulator of this process.


systematic_name: M341
exact_source: GSE10211_3064_200_DN
source_species_code: MM
GEO_id: GSE10211
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in tracheal epithelial cells infected with UV inactivated versus intact Sendai virus.

description_full:
  Oligonucleotide microarrays were used to establish a profile for gene expression in wild-type airway epithelial cells after paramyxoviral infection. Analysis was performed on mRNA isolated from SeV-infected primary-culture mouse tracheal epithelial cells that were maintained under physiologic conditions (air-liquid interface).


systematic_name: M343
exact_source: GSE10211_3064_200_UP
source_species_code: MM
GEO_id: GSE10211
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in tracheal epithelial cells infected with UV inactivated versus intact Sendai virus.

description_full:
  Oligonucleotide microarrays were used to establish a profile for gene expression in wild-type airway epithelial cells after paramyxoviral infection. Analysis was performed on mRNA isolated from SeV-infected primary-culture mouse tracheal epithelial cells that were maintained under physiologic conditions (air-liquid interface).


systematic_name: M344
exact_source: GSE10147_3523_200_UP
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells: IL3 [GeneID=3562] versus IL3 [GeneID=3562] and the HIV matrix protein p17.

description_full:
  We used microarrays to detail the global program of gene expression underlying the effect of p17 on human plasmacytoid dendritic cells and was compared to CpG profile.


systematic_name: M345
exact_source: GSE10147_3523_200_DN
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells: IL3 [GeneID=3562] versus IL3 [GeneID=3562] and the HIV matrix protein p17.

description_full:
  We used microarrays to detail the global program of gene expression underlying the effect of p17 on human plasmacytoid dendritic cells and was compared to CpG profile.


systematic_name: M348
exact_source: GSE10147_3524_200_UP
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells: IL3 [GeneID=3562] versus IL3 [GeneID=3562] and CpG.

description_full:
  We used microarrays to detail the global program of gene expression underlying the effect of p17 on human plasmacytoid dendritic cells and was compared to CpG profile.


systematic_name: M350
exact_source: GSE10147_3525_200_DN
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells treated with IL3 [GeneID=3562]: HIV matrix protein p17 versus CpG.

description_full:
[cell repeats an earlier one in this file: 167 characters]


systematic_name: M351
exact_source: GSE10147_3525_200_UP
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells treated with IL3 [GeneID=3562]: HIV matrix protein p17 versus CpG.

description_full:
[cell repeats an earlier one in this file: 167 characters]


systematic_name: M353
exact_source: GSE10147_3524_200_DN
source_species_code: HS
GEO_id: GSE10147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells: IL3 [GeneID=3562] versus IL3 [GeneID=3562] and CpG.

description_full:
[cell repeats an earlier one in this file: 167 characters]


systematic_name: M354
exact_source: GSE10422_2451_200_DN
source_species_code: MM
GEO_id: GSE10422
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype B cells versus BAFF-transgenic (over-express TNFSF13B [GeneID=10673]) B cells from lymph node.

description_full:
  Tumor necrosis factor-associated factors 2 and 3 (TRAF2 and TRAF3) were shown to function in a co-operative and non-redundant manner to suppress nuclear factor-κB2 (NF-κB2) activation, gene expression and survival in mature B cells. In the absence of this suppressive activity, B cells developed independently of the obligatory B cell survival factor, BAFF (B cell activating factor of the tumor necrosis factor family). This constitutive, lineage-specific suppression of B cell survival by TRAF2 and TRAF3 determines the requirement for BAFF to sustain B cell development in vivo. We wished to investigate the effect on gene expression in B cells which lacked the negative regulators TRAF2 and TRAF3, and hence had hyperactive NF-kB2 signalling. As Baff-tg mice display a similar phenotype, and have a genetic modification which acts in the same pathway, yet further up, than TRAF2 and TRAF3, we wished to compare and contrast Baff-tg B cells with TRAF2 and TRAF3 deficient B cells. This analysis should identify genes that are important in B cell survival.


systematic_name: M357
exact_source: GSE10422_2451_200_UP
source_species_code: MM
GEO_id: GSE10422
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype B cells versus BAFF-transgenic (over-express TNFSF13B [GeneID=10673]) B cells from lymph node.

description_full:
  Tumor necrosis factor-associated factors 2 and 3 (TRAF2 and TRAF3) were shown to function in a co-operative and non-redundant manner to suppress nuclear factor-κB2 (NF-κB2) activation, gene expression and survival in mature B cells. In the absence of this suppressive activity, B cells developed independently of the obligatory B cell survival factor, BAFF (B cell activating factor of the tumor necrosis factor family). This constitutive, lineage-specific suppression of B cell survival by TRAF2 and TRAF3 determines the requirement for BAFF to sustain B cell development in vivo. We wished to investigate the effect on gene expression in B cells which lacked the negative regulators TRAF2 and TRAF3, and hence had hyperactive NF-kB2 signalling. As Baff-tg mice display a similar phenotype, and have a genetic modification which acts in the same pathway, yet further up, than TRAF2 and TRAF3, we wished to compare and contrast Baff-tg B cells with TRAF2 and TRAF3 deficient B cells. This analysis should identify genes that are important in B cell survival.


description_full: Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages.
systematic_name: M358
exact_source: GSE10500_2635_200_UP
source_species_code: HS
GEO_id: GSE10500
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages from patients with synovial fluid rheumatoid arthritis versus monocyte-derived macrophages from healthy persons.


description_full: Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages.
systematic_name: M359
exact_source: GSE10500_2635_200_DN
source_species_code: HS
GEO_id: GSE10500
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages from patients with synovial fluid rheumatoid arthritis versus monocyte-derived macrophages from healthy persons.


systematic_name: M360
exact_source: GSE7568_2503_200_UP
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] and dexamethasone [PubChem=5743] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 3h.

description_full:
  The goal of the study was to identify the effects of TGF-beta on primary human macrophages maturated under different conditions.


systematic_name: M361
exact_source: GSE7568_2503_200_DN
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] and dexamethasone [PubChem=5743] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 3h.

description_full:
  The goal of the study was to identify the effects of TGF-beta on primary human macrophages maturated under different conditions.


systematic_name: M363
exact_source: GSE7568_2504_200_UP
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] and dexamethasone [PubChem=5743] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 24h.

description_full:
  The goal of the study was to identify the effects of TGF-beta on primary human macrophages maturated under different conditions.


systematic_name: M364
exact_source: GSE7568_2504_200_DN
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] and dexamethasone [PubChem=5743] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 24h.

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M365
exact_source: GSE7568_2505_200_UP
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 24h.

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M367
exact_source: GSE7568_2505_200_DN
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages differentiated in the presence of IL4 [GeneID=3565] for 5 days versus those subsequently treated with TGFB1 [GeneID=7040] for 24h.

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M368
exact_source: GSE7568_2506_200_UP
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages differentiated for 5 days in the presence of: IL4 [GeneID=3565] versus IL4 [GeneID=3565] and dexamethasone [PubChem=5743].

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M369
exact_source: GSE7568_2506_200_DN
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages differentiated for 5 days in the presence of: IL4 [GeneID=3565] versus IL4 [GeneID=3565] and dexamethasone [PubChem=5743].

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M370
exact_source: GSE7568_2507_200_UP
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages: 5 days with IL4 [GeneID=3565] and dexamethasone [PubChem=5743] followed by TGFB1 [GeneID=7040] for 24h versus 5 days with IL4 [GeneID=3565] followed by TGFB1 [GeneID=7040] for 24h.

description_full:
[cell repeats an earlier one in this file: 128 characters]


systematic_name: M371
exact_source: GSE7568_2507_200_DN
source_species_code: HS
GEO_id: GSE7568
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages: 5 days with IL4 [GeneID=3565] and dexamethasone [PubChem=5743] followed by TGFB1 [GeneID=7040] for 24h versus 5 days with IL4 [GeneID=3565] followed by TGFB1 [GeneID=7040] for 24h.

description_full:
[cell repeats an earlier one in this file: 128 characters]


description_brief: Genes down-regulated in B lymphocytes: naïve versus memory.
systematic_name: M372
exact_source: GSE11386_3027_200_DN
source_species_code: MM
GEO_id: GSE11386
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Memory B cells play essential roles in the maintenance of long-term immunity and may be important in the pathogenesis of autoimmune disease, but how these cells are distinguished from their naïve precursors is poorly understood. To address this, it would be important to understand how gene expression differs between memory and naive B cells in order to elucidate memory-specific functions. Using model systems that help overcome the lack of murine memory-specific markers and the low frequency of antigen-specific memory and naïve cells, we undertook a global comparison of gene expression between memory B cells and their naive precursors. 1st generation screen: These data represent our first generation comparison of gene expression between murine naïve and memory splenic B cells. Naïve NP-binding splenic B cells were FACS purified from unimmunized mVh186.2 transgenic Balb/c mice. Memory B cells were generated by immunizing mVh186.2 transgenic Balb/c mice with 2 doses of NP-CGG in alum delivered i.p. 6 weeks apart. After a minimum of 12-weeks rest, NP-binding splenic B cells were isolated by FACS. Total RNA was extracted, cRNA synthesized and labeled and hybridized to Affymetrix mouse 430 2.0 chips. 2nd generation screen: These data represent our second generation comparison of gene expression between murine naïve and memory splenic B cells. Naïve NP-binding AA4.1neg splenic B cells were FACS purified from unimmunized mVh186.2 transgenic Jk KO Balb/c mice. Memory B cells were generated from these naive precursors after adoptive transfer into recipients that mount poor endogenous NP-responses. 12-weeks post i.p. immunization with NP-CGG in alum, NP-specific splenic memory B cells were isolated by FACS. Total RNA was extracted, cRNA synthesized and labeled and hybridized to Affymetrix mouse 430 2.0 chips. Memory/Naïve comparison data linked below as Supplementary files.


description_brief: Genes up-regulated in dendritic cells: wildtype versus NFKB2 [GeneID=4791].
systematic_name: M377
exact_source: GSE7219_3082_200_UP
source_species_code: MM
GEO_id: GSE7219
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  This study aims at identifying genes that are NIK/NF-kappaB2 responsive in murine dendritic cells matured in vivo.


systematic_name: M383
exact_source: GSE7219_3084_200_UP
source_species_code: MM
GEO_id: GSE7219
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cell NIK NFkB2-KO versus dendritic cell NIK NFkB2-KO LPS and anti-CD40 stimulated.

description_full:
[cell repeats an earlier one in this file: 114 characters]


systematic_name: M384
exact_source: GSE7219_3084_200_DN
source_species_code: MM
GEO_id: GSE7219
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cell NIK NFkB2-KO versus dendritic cell NIK NFkB2-KO LPS and anti-CD40 stimulated.

description_full:
[cell repeats an earlier one in this file: 114 characters]


systematic_name: M385
exact_source: GSE7219_3085_200_UP
source_species_code: MM
GEO_id: GSE7219
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cell wildtype LPS and anti-CD40 stimulated versus dendritic cell NIK NFkB2-KO LPS and anti-CD40 stimulated.

description_full:
[cell repeats an earlier one in this file: 114 characters]


systematic_name: M386
exact_source: GSE7219_3085_200_DN
source_species_code: MM
GEO_id: GSE7219
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cell wildtype LPS and anti-CD40 stimulated versus dendritic cell NIK NFkB2-KO LPS and anti-CD40 stimulated.

description_full:
[cell repeats an earlier one in this file: 114 characters]


systematic_name: M387
exact_source: GSE12003_2896_200_UP
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in 4 day cultures of bone marrow progenitors: wildtype versus MIR223 [GeneID=407008] knockout.

description_full:
  This array analysis is to study developmental time course of the regulation of target messages’ expression during culture of murine neutrophils versus miR-223 null neutrophils. Culture media was SILAC-IMDM for MS analysis.


systematic_name: M388
exact_source: GSE11973_2666_200_UP
source_species_code: MM
GEO_id: GSE11973
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in neutrophils from MIR223 [GeneID=407008] bone marrow versus the wildtype cells.

description_full:
  This array analysis is to study the regulation of target messages’ expression in in vitro cultured murine neutrophils versus miR-223 null neutrophils. Culture media was SILAC-IMDM for MS analysis.


systematic_name: M390
exact_source: GSE12003_2896_200_DN
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in 4 day cultures of bone marrow progenitors: wildtype versus MIR223 [GeneID=407008] knockout.

description_full:
  This array analysis is to study developmental time course of the regulation of target messages’ expression during culture of murine neutrophils versus miR-223 null neutrophils. Culture media was SILAC-IMDM for MS analysis.


description_brief: Genes down-regulated in neutrophils: MIR223 [GeneID=407008] knockout versus wildtype.
systematic_name: M391
exact_source: GSE12001_2883_200_DN
source_species_code: MM
GEO_id: GSE12001
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  This array analysis is to study the regulation of target messages’ expression in murine neutrophils versus miR-223 null neutrophils.


systematic_name: M392
exact_source: GSE12003_2897_200_DN
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in 8 day cultures of bone marrow progenitors: wildtype versus MIR223 [GeneID=407008] knockout.

description_full:
  This array analysis is to study developmental time course of the regulation of target messages’ expression during culture of murine neutrophils versus miR-223 null neutrophils. Culture media was SILAC-IMDM for MS analysis.


systematic_name: M394
exact_source: GSE11973_2666_200_DN
source_species_code: MM
GEO_id: GSE11973
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in neutrophils from MIR223 [GeneID=407008] bone marrow versus the wildtype cells.

description_full:
  This array analysis is to study the regulation of target messages’ expression in in vitro cultured murine neutrophils versus miR-223 null neutrophils. Culture media was SILAC-IMDM for MS analysis.


systematic_name: M395
exact_source: GSE12003_2897_200_UP
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in 8 day cultures of bone marrow progenitors: wildtype versus MIR223 [GeneID=407008] knockout.

description_full:
[cell repeats an earlier one in this file: 222 characters]


systematic_name: M403
exact_source: GSE12003_2899_200_DN
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in of bone marrow progenitors with MIR223 [GeneID=407008] knockout: 4- versus 8-day cultures.

description_full:
[cell repeats an earlier one in this file: 222 characters]


systematic_name: M405
exact_source: GSE12003_2899_200_UP
source_species_code: MM
GEO_id: GSE12003
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in of bone marrow progenitors with MIR223 [GeneID=407008] knockout: 4- versus 8-day cultures.

description_full:
[cell repeats an earlier one in this file: 222 characters]


systematic_name: M407
exact_source: GSE11884_2701_200_UP
source_species_code: MM
GEO_id: GSE11884
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in naïve wildtype CD4 [GeneID=920] T cells versus those from T cell specific FURIN [GeneID=5045] knockout mice.

description_full:
  Furin is a proprotein convertase induced in activated T cells, reported to processes the anti-inflammatory cytokine TGFb-1. Herein, we show that conditional deletion of furin in T cells allowed for normal T cell development but impaired the function of regulatory T cells and effector cells, which produced less TGFb-1. Furin-deficient Treg cells, were less protective in a T cell transfer colitis model and failed to induce Foxp3 in normal T cells. Furin-deficient effector cells were inherently overly active and were resistant to suppressive activity of wild-type Tregs. Thus, our results indicate that furin is indispensable in maintaining peripheral tolerance, which is due, at least in part, to its nonredundant, essential function in regulating TGFb-1 production. Targeting furin has emerged as a strategy in malignant and infectious disease. The current work suggests that inhibiting furin might activate immune responses, but may result in a breakdown in peripheral tolerance.


systematic_name: M410
exact_source: GSE11884_2701_200_DN
source_species_code: MM
GEO_id: GSE11884
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in naïve wildtype CD4 [GeneID=920] T cells versus those from T cell specific FURIN [GeneID=5045] knockout mice.

description_full:
  Furin is a proprotein convertase induced in activated T cells, reported to processes the anti-inflammatory cytokine TGFb-1. Herein, we show that conditional deletion of furin in T cells allowed for normal T cell development but impaired the function of regulatory T cells and effector cells, which produced less TGFb-1. Furin-deficient Treg cells, were less protective in a T cell transfer colitis model and failed to induce Foxp3 in normal T cells. Furin-deficient effector cells were inherently overly active and were resistant to suppressive activity of wild-type Tregs. Thus, our results indicate that furin is indispensable in maintaining peripheral tolerance, which is due, at least in part, to its nonredundant, essential function in regulating TGFb-1 production. Targeting furin has emerged as a strategy in malignant and infectious disease. The current work suggests that inhibiting furin might activate immune responses, but may result in a breakdown in peripheral tolerance.


description_brief: Genes down-regulated in T reg: wildtype versus DICER1 [GeneID=23405] knockout.
systematic_name: M411
exact_source: GSE11818_3401_200_DN
source_species_code: MM
GEO_id: GSE11818
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  A new Treg-specific, FoxP3-GFP-hCre BAC transgenic was crossed to a conditional Dicer knock-out mouse strain to analyze the role of microRNAs (miRNA) in the development and function of regulatory T cells (Tregs). Although thymic Tregs developed normally in this setting, the cells showed evidence of altered differentiation and dysfunction in the periphery. Dicer-deficient Treg lineage cells failed to remain stable as a subset of cells down-regulated the Treg-specific transcription factor, FoxP3, while the majority expressed altered levels of multiple genes and proteins (including Neuropilin 1, GITR and CTLA-4) associated with the Treg fingerprint. In fact, a significant percentage of the Treg lineage cells took on a Th memory phenotype including increased levels of CD127, IL-4, and interferon-g. Importantly, Dicer-deficient Tregs lost suppression activity in vivo; the mice rapidly developed fatal systemic autoimmune disease resembling the FoxP3 knockout phenotype. These results support a central role for miRNAs in maintaining the stability of differentiated Treg function in vivo and homeostasis of the adaptive immune system.


description_brief: Genes up-regulated in dendritic cells: immature versus mature stimulatory.
systematic_name: M415
exact_source: GSE9946_2753_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Myeloid dendritic cells (DC) and macrophages play an important role in pathogen sensing and antimicrobial defense. Recently we demonstrated that infection of human DC with intracellular bacterium Listeria monocytogenes (L.monocytogenes) leads to the induction of the immunoinhibitory enzyme indoleamine 2,3-dioxygenase (Popov et al., J Clin Invest, 2006), while in the previous studies L.monocytogenes infection was associated with a rather stimulatory DC phenotype. To clarify this discrepancy we performed comparative microarray analysis of immature mo-DC (immDC), mature stimulatory mo-DC (matDC) and mature inhibitory DC either stimulated with prostaglandin E2 (PGE2-DC) or infected with L.monocytogenes (infDC). Studying infection of human myeloid DC with Listeria monocytogenes, we found out, that infected DC are modified by the pathogen to express multiple inhibitory molecules, including indoleamine 2,3-dioxygenase (IDO), cyclooxygenase-2, interleukin 10 and CD25, which acts on DC as IL-2 scavenger. All these inhibitory molecules, expressed on regulatory DC (DCreg), are strictly TNF-dependent and are in concert suppressing T-cell responses. Moreover, only DCreg can efficiently control the number of intracellular listeria, mostly by IDO-mediated mechanisms and by other factors, remaining to be identified. Analyzing publicly acessible data of transcriptional changes in DC and macrophages, infected by various pathogens and parasites (GEO, GSE360), we noticed that infection of these cells with Mycobacterium tuberculosis causes transcriptional response, comparable with the one caused by listeria in human DC. In fact, granuloma in tuberculosis and listeriosis in vivo are enriched for myeloid DC and macrophages characterized by regulatory phenotype. In summary, regulatory myeloid DC and macrophages may play a dual role during life-threatening granulomatous infections, such as tuberculosis: on one hand, regulatory myeloid cells promote pathogen containment by efficiently killing intracellular bacteria, on the other hand these cells inhibit granuloma-associated T cells and thereby might be involved in the retention of TNF-controlled granuloma integrity protecting the host from granuloma break-down and pathogen dissemination.


systematic_name: M418
exact_source: GSE9946_2754_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cells: immature versus mature inhibitory infected with L. monocytogenes.

description_full:
  Myeloid dendritic cells (DC) and macrophages play an important role in pathogen sensing and antimicrobial defense. Recently we demonstrated that infection of human DC with intracellular bacterium Listeria monocytogenes (L.monocytogenes) leads to the induction of the immunoinhibitory enzyme indoleamine 2,3-dioxygenase (Popov et al., J Clin Invest, 2006), while in the previous studies L.monocytogenes infection was associated with a rather stimulatory DC phenotype. To clarify this discrepancy we performed comparative microarray analysis of immature mo-DC (immDC), mature stimulatory mo-DC (matDC) and mature inhibitory DC either stimulated with prostaglandin E2 (PGE2-DC) or infected with L.monocytogenes (infDC). Studying infection of human myeloid DC with Listeria monocytogenes, we found out, that infected DC are modified by the pathogen to express multiple inhibitory molecules, including indoleamine 2,3-dioxygenase (IDO), cyclooxygenase-2, interleukin 10 and CD25, which acts on DC as IL-2 scavenger. All these inhibitory molecules, expressed on regulatory DC (DCreg), are strictly TNF-dependent and are in concert suppressing T-cell responses. Moreover, only DCreg can efficiently control the number of intracellular listeria, mostly by IDO-mediated mechanisms and by other factors, remaining to be identified. Analyzing publicly acessible data of transcriptional changes in DC and macrophages, infected by various pathogens and parasites (GEO, GSE360), we noticed that infection of these cells with Mycobacterium tuberculosis causes transcriptional response, comparable with the one caused by listeria in human DC. In fact, granuloma in tuberculosis and listeriosis in vivo are enriched for myeloid DC and macrophages characterized by regulatory phenotype. In summary, regulatory myeloid DC and macrophages may play a dual role during life-threatening granulomatous infections, such as tuberculosis: on one hand, regulatory myeloid cells promote pathogen containment by efficiently killing intracellular bacteria, on the other hand these cells inhibit granuloma-associated T cells and thereby might be involved in the retention of TNF-controlled granuloma integrity protecting the host from granuloma break-down and pathogen dissemination.


systematic_name: M420
exact_source: GSE9946_2754_200_DN
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells: immature versus mature inhibitory infected with L. monocytogenes.

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M421
exact_source: GSE9946_2755_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cells: immature versus mature inhibitory treated by prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M422
exact_source: GSE9946_2755_200_DN
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells: immature versus mature inhibitory treated by prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M423
exact_source: GSE9946_2756_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mature dendritic cells: stimulatory versus inhibitory infected with L. monocytogenes.

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M425
exact_source: GSE9946_2756_200_DN
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mature dendritic cells: stimulatory versus inhibitory infected with L. monocytogenes.

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M428
exact_source: GSE9946_2757_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mature dendritic cells: stimulatory versus inhibitory treated by prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M429
exact_source: GSE9946_2757_200_DN
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mature dendritic cells: stimulatory versus inhibitory treated by prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M430
exact_source: GSE9946_2758_200_UP
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mature inhibitory dendritic cells: L. monocytogenes infection versus prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


systematic_name: M431
exact_source: GSE9946_2758_200_DN
source_species_code: HS
GEO_id: GSE9946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mature inhibitory dendritic cells: L. monocytogenes infection versus prostaglandin E2 [PubChem=5280360].

description_full:
[cell repeats an earlier one in this file: 2251 characters]


description_brief: Genes down-regulated in neutrophils isolated from: healthy versus patients with peridontitis.
systematic_name: M432
exact_source: GSE12484_2752_200_DN
source_species_code: HS
GEO_id: GSE12484
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Peripheral blood neutrophils from periodontitis patients exhibit a hyper-reactive and hyper-active phenotype (collectively termed hyper-responsivity) in terms of production of reactive oxygen species (ROS) however the molecular basis for this observation is yet to be determined. Our objectives were to identify genes differentially expressed in hyper-responsive peripheral blood neutrophils from chronic periodontitis patients relative to periodontally healthy controls and use this data to identify potential contributory pathways to the hyper-responsive neutrophil phenotype.


description_brief: Genes down-regulated in tymocytes: mutant (hypomorph) ATG16L1 [GeneID=55054] versus wildtype.
systematic_name: M434
exact_source: GSE12707_2700_200_DN
source_species_code: MM
GEO_id: GSE12707
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The aim of this study is to survey global gene expression of total thymocytes from wild-type mice and Atg16l1 mutant (hypomorph) mice.


systematic_name: M437
exact_source: GSE12505_2251_200_UP
source_species_code: MM
GEO_id: GSE12505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells: wildtype versus TCF4 [GeneID=6925] heterozygous knockout.

description_full:
  Analysis of expression profiles of pDCs from wild type and heterozygous E2-2 mice. Results show the control by E2-2 of the expression of pDC-enriched genes.


description_brief: Genes up-regulated in CAL1 cells (plasmacytoid dendritic cells) versus MOLT4 (immature T cells).
systematic_name: M438
exact_source: GSE12507_2252_200_UP
source_species_code: HS
GEO_id: GSE12507
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Analysis of expression profiles of human pDC cell line (CAL1) compared to an immature T cell line (MOLT4)


systematic_name: M439
exact_source: GSE12505_2251_200_DN
source_species_code: MM
GEO_id: GSE12505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells: wildtype versus TCF4 [GeneID=6925] heterozygous knockout.

description_full:
  Analysis of expression profiles of pDCs from wild type and heterozygous E2-2 mice. Results show the control by E2-2 of the expression of pDC-enriched genes.


description_brief: Genes down-regulated in peripheral blood monocytes (PBMC): control versus IL-12 stimulation.
systematic_name: M441
exact_source: GSE12839_2401_200_DN
source_species_code: HS
GEO_id: GSE12839
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The cytokine interleukin-12 (IL-12) is known to play a central role in adaptive and innate immunity. We employed microarray analysis of IL-12 induced gene expression to provide further insights into its effects on immune response.


systematic_name: M447
exact_source: GSE12963_2629_200_UP
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in control CD4 [GeneID=920] T cells versus those infected with HIV-1 viruses lacking Env, Vpr and Nef.

description_full:
  The high mutation rate of HIV is linked to the generation of viruses expressing proteins with altered function whose impact on disease progression is unknown. We investigated the effects of HIV-1 viruses lacking Env, Vpr and Nef on CD4+ T cell gene expression using high-density DNA microarray analysis and functional assays.


systematic_name: M448
exact_source: GSE12963_2629_200_DN
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in control CD4 [GeneID=920] T cells versus those infected with HIV-1 viruses lacking Env, Vpr and Nef.

description_full:
  The high mutation rate of HIV is linked to the generation of viruses expressing proteins with altered function whose impact on disease progression is unknown. We investigated the effects of HIV-1 viruses lacking Env, Vpr and Nef on CD4+ T cell gene expression using high-density DNA microarray analysis and functional assays.


systematic_name: M449
exact_source: GSE12963_2628_200_UP
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in control CD4 [GeneID=920] T cells versus those infected with HIV-1 viruses lacking Env and Nef.

description_full:
  The high mutation rate of HIV is linked to the generation of viruses expressing proteins with altered function whose impact on disease progression is unknown. We investigated the effects of HIV-1 viruses lacking Env, Vpr and Nef on CD4+ T cell gene expression using high-density DNA microarray analysis and functional assays.


systematic_name: M452
exact_source: GSE12963_2628_200_DN
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in control CD4 [GeneID=920] T cell versus those infected with HIV-1 viruses lacking Env and Nef.

description_full:
[cell repeats an earlier one in this file: 325 characters]


systematic_name: M455
exact_source: GSE12963_2630_200_UP
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells infected with Env/Nef deficient HIV-1 viruses versus those infected with HIV-1 viruses lacking Env, Nef and Vpr.

description_full:
[cell repeats an earlier one in this file: 325 characters]


systematic_name: M458
exact_source: GSE12963_2630_200_DN
source_species_code: HS
GEO_id: GSE12963
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells infected with Env/Nef deficient HIV-1 viruses versus those infected with HIV-1 viruses lacking Env, Nef and Vpr.

description_full:
[cell repeats an earlier one in this file: 325 characters]


systematic_name: M460
exact_source: GSE11367_3380_200_UP
source_species_code: HS
GEO_id: GSE11367
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in vascular smooth muscle cells: control versus treated with IL17A [GeneID=3605].

description_full:
  Investigate the effect of recombinant human IL-17A on vascular smooth muscle cells cultured from human aortas.


systematic_name: M461
exact_source: GSE11367_3380_200_DN
source_species_code: HS
GEO_id: GSE11367
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in vascular smooth muscle cells: control versus treated with IL17A [GeneID=3605].

description_full:
  Investigate the effect of recombinant human IL-17A on vascular smooth muscle cells cultured from human aortas.


description_brief: Genes up-regulated in CD4 [GeneID=920] T cells: control versus IL6 [GeneID=3569].
systematic_name: M462
exact_source: GSE7459_2237_200_UP
source_species_code: MM
GEO_id: GSE7459
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  IL-6, a proinflammtory cytokine produced by antigen presenting cells and non-hematopoietic cells in response to external stimuli, acts as an important bridge between the innate and adaptive immune responses. IL-6 together with IL-4 can promote Th2 polarization, while in combination with TGFbeta mediates Th17 differentiation. We examined early changes in gene expression in mouse CD4+ T cells induced by IL-6.


description_brief: Genes up-regulated in NIH3T3 cells (fibroblast): control versus stimulated with IFN-b.
systematic_name: M466
exact_source: GSE14413_1127_200_UP
source_species_code: MM
GEO_id: GSE14413
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Cytoplasmic DNA triggers the activation of the innate immune system. While downstream signaling components have been characterized, the DNA sensing components remain largely elusive. We performed a systematic proteomics screen for proteins that associate with DNA, traversed to a screen for IFN-β-induced transcripts. We identified DSIRE (DNA sensor for the IL-1β response, previously called AIM2) as a candidate cytoplasmic sensor. DSIRE showed a marked selectivity for double-stranded DNA. DSIRE can recruit the inflammasome adaptor ASC and gets redistributed to ASC speckles upon coexpression of ASC. RNAi-mediated reduction of DSIRE expression led to an impairment in IL-1β maturation. Reconstitution of unresponsive cells with DSIRE, ASC, caspase 1 and IL-1β showed that DSIRE is sufficient for inflammasome activation. Overall, our data strongly suggest that DSIRE is a cytoplasmic DNA sensor for the inflammasome.


systematic_name: M474
exact_source: GSE13887_2807_200_DN
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from healthy donors: activated by anti-CD3 and anti-CD28 versus nitric oxide [PubChem=145068] treatment.

description_full:
  CD3-positive T cells were negatively isolated from 10 SLE patients and 9 healthy controls without SLE. All of the SLE samples and control samples were compared with one another to identify baseline differences in expression due to the disease. Next, T cell preparations from 4 of the control subjects were stimulated with either Nitric Oxide (NOC-18) 600 uM for 24hr or stimulated through CD3/CD28 for 24hr to determine which genes were responsive to these signaling mechanisms. Here, we show that activity of the mammalian target of rapamycin (mTOR), which is a sensor of the mitochondrial transmembrane potential, is increased in SLE T cells. Activation of mTOR was inducible by NO, a key trigger of MHP which in turn enhanced the expression of HRES-1/Rab4, a small GTPase that regulates recycling of surface receptors through early endosomes. Expression of HRES-1/Rab4 was increased in SLE T cells and, in accordance with its dominant impact on the endocytic recycling of CD4, it was inversely correlated with diminished CD4 expression. HRES-1/Rab4 over-expression was also inversely correlated with diminished TCRζ protein levels. Combined with follow up studies, these results suggest that activation of mTOR causes the loss of TCRζ in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation.


systematic_name: M475
exact_source: GSE13887_2804_200_DN
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in resting CD4 [GeneID=920] T cells: healthy versus systemic lupus erythrematosus (SLE).

description_full:
  CD3-positive T cells were negatively isolated from 10 SLE patients and 9 healthy controls without SLE. All of the SLE samples and control samples were compared with one another to identify baseline differences in expression due to the disease. Next, T cell preparations from 4 of the control subjects were stimulated with either Nitric Oxide (NOC-18) 600 uM for 24hr or stimulated through CD3/CD28 for 24hr to determine which genes were responsive to these signaling mechanisms. Here, we show that activity of the mammalian target of rapamycin (mTOR), which is a sensor of the mitochondrial transmembrane potential, is increased in SLE T cells. Activation of mTOR was inducible by NO, a key trigger of MHP which in turn enhanced the expression of HRES-1/Rab4, a small GTPase that regulates recycling of surface receptors through early endosomes. Expression of HRES-1/Rab4 was increased in SLE T cells and, in accordance with its dominant impact on the endocytic recycling of CD4, it was inversely correlated with diminished CD4 expression. HRES-1/Rab4 over-expression was also inversely correlated with diminished TCRζ protein levels. Combined with follow up studies, these results suggest that activation of mTOR causes the loss of TCRζ in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation.


systematic_name: M478
exact_source: GSE13887_2805_200_UP
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from healthy donors: resting versus activated by anti-CD3 and anti-CD28.

description_full:
  CD3-positive T cells were negatively isolated from 10 SLE patients and 9 healthy controls without SLE. All of the SLE samples and control samples were compared with one another to identify baseline differences in expression due to the disease. Next, T cell preparations from 4 of the control subjects were stimulated with either Nitric Oxide (NOC-18) 600 uM for 24hr or stimulated through CD3/CD28 for 24hr to determine which genes were responsive to these signaling mechanisms. Here, we show that activity of the mammalian target of rapamycin (mTOR), which is a sensor of the mitochondrial transmembrane potential, is increased in SLE T cells. Activation of mTOR was inducible by NO, a key trigger of MHP which in turn enhanced the expression of HRES-1/Rab4, a small GTPase that regulates recycling of surface receptors through early endosomes. Expression of HRES-1/Rab4 was increased in SLE T cells and, in accordance with its dominant impact on the endocytic recycling of CD4, it was inversely correlated with diminished CD4 expression. HRES-1/Rab4 over-expression was also inversely correlated with diminished TCRζ protein levels. Combined with follow up studies, these results suggest that activation of mTOR causes the loss of TCRζ in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation.


systematic_name: M479
exact_source: GSE13887_2806_200_DN
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from healthy donors: resting versus nitric oxide [PubChem=145068].

description_full:
[cell repeats an earlier one in this file: 1307 characters]


systematic_name: M481
exact_source: GSE13887_2807_200_UP
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from healthy donors: activated by anti-CD3 and anti-CD28 versus nitric oxide [PubChem=145068] treatment.

description_full:
[cell repeats an earlier one in this file: 1307 characters]


systematic_name: M484
exact_source: GSE13887_2805_200_DN
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from healthy donors: resting versus activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 1307 characters]


systematic_name: M485
exact_source: GSE13887_2806_200_UP
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from healthy donors: resting versus nitric oxide [PubChem=145068].

description_full:
[cell repeats an earlier one in this file: 1307 characters]


systematic_name: M1889
exact_source: GSE13887_2804_200_UP
source_species_code: HS
GEO_id: GSE13887
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in resting CD4 [GeneID=920] T cells: healthy versus systemic lupus erythrematosus (SLE).

description_full:
[cell repeats an earlier one in this file: 1307 characters]


systematic_name: M1891
exact_source: GSE13762_3470_200_DN
source_species_code: HS
GEO_id: GSE13762
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells (5 days): control versus 25-hydroxyvitamin D3 [PubChem=1593].

description_full:
  We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells.


systematic_name: M1892
exact_source: GSE13762_3471_200_UP
source_species_code: HS
GEO_id: GSE13762
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cells (12 days): control versus 25-hydroxyvitamin D3 [PubChem=1593].

description_full:
  We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells.


systematic_name: M1896
exact_source: GSE13762_3471_200_DN
source_species_code: HS
GEO_id: GSE13762
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells (12 days): control versus 25-hydroxyvitamin D3 [PubChem=1593].

description_full:
[cell repeats an earlier one in this file: 657 characters]


description_brief: Genes down-regulated in skin from: wildtype (BALB/c) versus IFNG [GeneID=3458] knockout.
systematic_name: M1898
exact_source: GSE13522_3071_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  To investigate the early host response triggered by three different strains of Trypanosoma cruzi at a local infection site, changes in host gene expression were monitored in a murine intradermal infection model using Affymetrix oligonucleotide arrays. Robust induction of IFN-stimulated genes (ISGs) was observed in excised skin 24 hours post-infection where the level of ISG induction was parasite strain-dependent with the least virulent strain triggering a muted IFN response. Infection of mice immunodepleted of IFNγ-producing cells or infection of IFNγ-deficient mice had minimal impact on the IFN response generated in T. cruzi infected mice. In contrast, infection of mice lacking the type I IFN receptor demonstrated that type I IFNs are largely responsible for the IFN response generated at the site of infection. These data highlight type I IFNs as important components of the innate immune response to T. cruzi the site of inoculation and their role in shaping the early transcriptional response to this pathogen. We used microarrays to detail the local host transcriptional response to intradermal T. cruzi infection in WT mice and mice depleted of NK cells, or deficient in IFN-gamma or type I IFN responses. Additionally we compared the local host-transcriptional response generated to infection with 3 different strains of Trypanosoma cruzi (Y, Brazil, and G).


systematic_name: M2906
exact_source: GSE13522_3068_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
  To investigate the early host response triggered by three different strains of Trypanosoma cruzi at a local infection site, changes in host gene expression were monitored in a murine intradermal infection model using Affymetrix oligonucleotide arrays. Robust induction of IFN-stimulated genes (ISGs) was observed in excised skin 24 hours post-infection where the level of ISG induction was parasite strain-dependent with the least virulent strain triggering a muted IFN response. Infection of mice immunodepleted of IFNγ-producing cells or infection of IFNγ-deficient mice had minimal impact on the IFN response generated in T. cruzi infected mice. In contrast, infection of mice lacking the type I IFN receptor demonstrated that type I IFNs are largely responsible for the IFN response generated at the site of infection. These data highlight type I IFNs as important components of the innate immune response to T. cruzi the site of inoculation and their role in shaping the early transcriptional response to this pathogen. We used microarrays to detail the local host transcriptional response to intradermal T. cruzi infection in WT mice and mice depleted of NK cells, or deficient in IFN-gamma or type I IFN responses. Additionally we compared the local host-transcriptional response generated to infection with 3 different strains of Trypanosoma cruzi (Y, Brazil, and G).


systematic_name: M2908
exact_source: GSE13522_3069_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain Brazil).

description_full:
  To investigate the early host response triggered by three different strains of Trypanosoma cruzi at a local infection site, changes in host gene expression were monitored in a murine intradermal infection model using Affymetrix oligonucleotide arrays. Robust induction of IFN-stimulated genes (ISGs) was observed in excised skin 24 hours post-infection where the level of ISG induction was parasite strain-dependent with the least virulent strain triggering a muted IFN response. Infection of mice immunodepleted of IFNγ-producing cells or infection of IFNγ-deficient mice had minimal impact on the IFN response generated in T. cruzi infected mice. In contrast, infection of mice lacking the type I IFN receptor demonstrated that type I IFNs are largely responsible for the IFN response generated at the site of infection. These data highlight type I IFNs as important components of the innate immune response to T. cruzi the site of inoculation and their role in shaping the early transcriptional response to this pathogen. We used microarrays to detail the local host transcriptional response to intradermal T. cruzi infection in WT mice and mice depleted of NK cells, or deficient in IFN-gamma or type I IFN responses. Additionally we compared the local host-transcriptional response generated to infection with 3 different strains of Trypanosoma cruzi (Y, Brazil, and G).


systematic_name: M2910
exact_source: GSE13522_3072_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin from INFG [GeneID=3458] knockout mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2911
exact_source: GSE13522_3073_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (BALB/c) versus INFG [GeneID=3458] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2912
exact_source: GSE13522_3070_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain G).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2914
exact_source: GSE13522_3072_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin from INFG [GeneID=3458] knockout mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2915
exact_source: GSE13522_3073_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (BALB/c) versus INFG [GeneID=3458] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2916
exact_source: GSE13522_3074_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin from 129S1 mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2917
exact_source: GSE13522_3074_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin from 129S1 mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2918
exact_source: GSE13522_3077_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (BALB/c) versus IFNAR1 [GeneID=3454] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2921
exact_source: GSE13522_3069_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain Brazil).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2922
exact_source: GSE13522_3070_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain G).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2928
exact_source: GSE13522_3068_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin from BALB/c mice after injection of: control versus Trypanosoma cruzi (strain Y).

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2929
exact_source: GSE13522_3075_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (129S1) versus IFNAR1 [GeneID=3454] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2930
exact_source: GSE13522_3075_200_DN
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (129S1) versus IFNAR1 [GeneID=3454] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


systematic_name: M2933
exact_source: GSE13522_3077_200_UP
source_species_code: MM
GEO_id: GSE13522
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in skin after injection of Trypanosoma cruzi (strain Y): wildtype (BALB/c) versus IFNAR1 [GeneID=3454] knockout.

description_full:
[cell repeats an earlier one in this file: 1375 characters]


description_brief: Genes up-regulated in CD8 T cells: naïve versus activated.
systematic_name: M2934
exact_source: GSE14699_3151_200_UP
source_species_code: MM
GEO_id: GSE14699
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Peripheral tolerance induction is critical for the maintenance of self-tolerance and can be mediated by immunoregulatory T cells or by direct induction of T cell anergy or deletion. While the molecular processes underlying anergy have been extensively studied, little is known about the molecular basis for peripheral T cell deletion. Here, we determined the gene expression signature of peripheral CD8+ T cells undergoing deletional tolerance, relative to those undergoing immunogenic priming or lymphopenia-induced proliferation. From these data, we report the first detailed molecular signature of cells undergoing deletion. Consistent with defective cytolysis, these cells exhibited deficiencies in granzyme up-regulation. Furthermore, they showed antigen-driven Bcl-2 down-regulation and early up-regulation of the pro-apoptotic protein Bim, consistent with the requirement of this BH3-only protein for peripheral T cell deletion. Bim up-regulation was paralleled by defective IL-7Ra chain re-expression, suggesting that Bim-dependent death may be triggered by loss of IL-7/IL-7R signaling. Finally, we observed parallels in molecular signatures between deletion and anergy suggesting that these tolerance pathways may not be as molecularly distinct as previously surmised.


systematic_name: M2942
exact_source: GSE13946_3828_200_DN
source_species_code: MM
GEO_id: GSE13946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in gamma delta intraepithelial lymphocytes from colon: control versus colitis induced by dextran sulfate sodium (DSS).

description_full:
  gamma delta intraepithelial lymphocytes were isolated from the colons of DSS-treated and untreated mice. Total RNAs were isolated and compared by Affymetrix DNA microarray.


systematic_name: M2943
exact_source: GSE13946_3828_200_UP
source_species_code: MM
GEO_id: GSE13946
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in gamma delta intraepithelial lymphocytes from colon: control versus colitis induced by dextran sulfate sodium (DSS).

description_full:
  gamma delta intraepithelial lymphocytes were isolated from the colons of DSS-treated and untreated mice. Total RNAs were isolated and compared by Affymetrix DNA microarray.


description_brief: Genes up-regulated in activated T lymphocytes: T conv versus natural T reg.
systematic_name: M2945
exact_source: GSE14415_2981_200_UP
source_species_code: MM
GEO_id: GSE14415
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The gene expression profile of peripheral Foxp3+ natural regulatory T cells isolated from Foxp3/EGFP bicistronic mice was compared to that of in vitro-induced regulatory T cells and to CD4+ conventional (Foxp3-) T cells. The role of the regulatory T cell transcription factor Foxp3 in shaping the transcriptosomes of natural and induced regulatory T cells was analyzed using mice expressing a mutant FOXP3-EGFP fusion protein (Foxp3deltaEGFP). We used gene expression microarrays to examine the transcriptional programs of natural and induced regulatory T cells and the function of Foxp3 in organizing the transcriptosomes of the respective cell type


systematic_name: M2954
exact_source: GSE14415_2987_200_UP
source_species_code: MM
GEO_id: GSE14415
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in induced T reg cultured with IL2 [GeneID=3558]: wildtype versus non-functional FOXP3 [GeneID=50943].

description_full:
[cell repeats an earlier one in this file: 650 characters]


systematic_name: M2956
exact_source: GSE14415_2987_200_DN
source_species_code: MM
GEO_id: GSE14415
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in induced T reg cultured with IL2 [GeneID=3558]: wildtype versus non-functional FOXP3 [GeneID=50943].

description_full:
[cell repeats an earlier one in this file: 650 characters]


systematic_name: M2977
exact_source: GSE14386_2514_200_UP
source_species_code: HS
GEO_id: GSE14386
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in peripheral blood mononclear cells (PBMC) from multiple sclerosis (MS) patient: untreated versus IFNB1 [GeneID=3456].

description_full:
  IFNβ, an effective therapy against relapsing-remitting (RR) multiple sclerosis (MS) is naturally secreted during the innate immune response against viral pathogens. The objective of this study was to characterize the immunomodulatory mechanisms of IFNβ targeting innate immune response and their effects on DC-mediated regulation of T-cell differentiation. We found that IFNβ−1a in-vitro treatment of human monocyte-derived dendritic cells (DCs) induced the expression of TLR7 and the members of its downstream signaling pathway, including myeloid differentiation factor 88 (MyD88), IL-1R-associated kinase (IRAK)4, and TNF receptor-associated factor (TRAF)6, while it inhibited the expression of IL-1R. Using siRNA TLR7 gene silencing, we confirmed that IFNβ-1a-induced changes in MyD88, IRAK4 and IL-1R expression were dependent on TLR7. TLR7 expression was also necessary for the IFNβ-1a-induced inhibition of IL-1β and IL-23, and the induction of IL-27 secretion by DCs. Supernatant (SN) transfer experiments confirmed that IFNβ-1a-induced changes in DCs’ cytokine secretion inhibit Th17 cell differentiation as evidenced by the inhibition of retinoic acid-related orphan nuclear hormone receptor C (RORC) and IL-17A gene expression and IL-17A secretion. Our study has identified a novel therapeutic mechanism of IFNβ−1a, that selectively targets the autoimmune response in MS.


systematic_name: M2979
exact_source: GSE14386_2514_200_DN
source_species_code: HS
GEO_id: GSE14386
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in peripheral blood mononclear cells (PBMC) from multiple sclerosis (MS) patient: untreated versus IFNB1 [GeneID=3456].

description_full:
  IFNβ, an effective therapy against relapsing-remitting (RR) multiple sclerosis (MS) is naturally secreted during the innate immune response against viral pathogens. The objective of this study was to characterize the immunomodulatory mechanisms of IFNβ targeting innate immune response and their effects on DC-mediated regulation of T-cell differentiation. We found that IFNβ−1a in-vitro treatment of human monocyte-derived dendritic cells (DCs) induced the expression of TLR7 and the members of its downstream signaling pathway, including myeloid differentiation factor 88 (MyD88), IL-1R-associated kinase (IRAK)4, and TNF receptor-associated factor (TRAF)6, while it inhibited the expression of IL-1R. Using siRNA TLR7 gene silencing, we confirmed that IFNβ-1a-induced changes in MyD88, IRAK4 and IL-1R expression were dependent on TLR7. TLR7 expression was also necessary for the IFNβ-1a-induced inhibition of IL-1β and IL-23, and the induction of IL-27 secretion by DCs. Supernatant (SN) transfer experiments confirmed that IFNβ-1a-induced changes in DCs’ cytokine secretion inhibit Th17 cell differentiation as evidenced by the inhibition of retinoic acid-related orphan nuclear hormone receptor C (RORC) and IL-17A gene expression and IL-17A secretion. Our study has identified a novel therapeutic mechanism of IFNβ−1a, that selectively targets the autoimmune response in MS.


description_brief: Genes down-regulated in B lymphocytes: control versus stimulated by anti-IgM for 12h.
systematic_name: M2980
exact_source: GSE13547_3163_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The development, homeostasis and function of B lymphocytes involve multiple rounds of B cell receptor (BCR)-controlled proliferation and prolonged maintenance. We analyzed the role of transcription factor Zfx, a recently identified regulator of stem cell maintenance, in B cell development and homeostasis. Conditional Zfx deletion in the bone marrow blocked B cell development at the pre-BCR selection checkpoint. Zfx deficiency in peripheral B cells caused impaired generation of the B-1 cell lineage, accelerated B cell turnover, depletion of mature recirculating cells, and delayed T-dependent antibody responses. Zfx-deficient B cells showed normal proximal BCR signaling, but impaired BCR-induced proliferation and survival. This was accompanied by aberrantly enhanced and prolonged integrated stress response, and delayed induction of Cyclin D2 and Bcl-xL proteins. Thus, Zfx restrains the stress response and couples antigen receptor signaling to B cell expansion and maintenance during development and peripheral homeostasis.


systematic_name: M2983
exact_source: GSE13547_3170_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes stimulated by anti-IgM for 12h: wildtype versus ZFX [GeneID=7543] knockout.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2988
exact_source: GSE13547_3169_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes stimulated by anti-IgM for 2h: wildtype versus ZFX [GeneID=7543] knockout.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2989
exact_source: GSE13547_3170_200_UP
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes stimulated by anti-IgM for 12h: wildtype versus ZFX [GeneID=7543] knockout.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2990
exact_source: GSE13547_3165_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes with ZFX [GeneID=7543] knockout: control versus stimulated by anti-IgM for 2h.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2994
exact_source: GSE13547_3169_200_UP
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes stimulated by anti-IgM for 2h: wildtype versus ZFX [GeneID=7543] knockout.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2995
exact_source: GSE13547_3167_200_UP
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes stimulated by anti-IgM: ZFX [GeneID=7543] knockout (2h) versus wildtype (12h).

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M2996
exact_source: GSE13547_3167_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes stimulated by anti-IgM: ZFX [GeneID=7543] knockout (2h) versus wildtype (12h).

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M3000
exact_source: GSE13547_3165_200_UP
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes with ZFX [GeneID=7543] knockout: control versus stimulated by anti-IgM for 2h.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M7001
exact_source: GSE13547_3166_200_UP
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes: ZFX [GeneID=7543] knockout versus wildtype cells stimulated by anti-IgM for 12h.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


systematic_name: M7002
exact_source: GSE13547_3166_200_DN
source_species_code: MM
GEO_id: GSE13547
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes: ZFX [GeneID=7543] knockout versus wildtype cells stimulated by anti-IgM for 12h.

description_full:
[cell repeats an earlier one in this file: 1034 characters]


description_brief: Genes up-regulated in hematopoietic stem cells versus megakaryo-erythrocyte progenitors.
systematic_name: M7005
exact_source: GSE15330_2817_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Regulation of lineage potential and transcriptional priming by Ikaros. New insight is provided into a bivalent regulation of lineage priming in the HSC and its lympho-myeloid restricted progeny the LMPP by the lymphoid lineage-determining factor Ikaros Whereas Ikaros is responsible for the activation of a cascade of lymphoid expression programs and for the establishment of lymphoid potential from the HSC to the LMPP it is also responsible for the repression of stem cell and erythroid genetic programs that are incompatible with further lineage restrictions emanating from the LMPP


systematic_name: M7009
exact_source: GSE15330_2834_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: lymphoid-primed multipotent progenitors versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7010
exact_source: GSE15330_2834_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: lymphoid-primed multipotent progenitors versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7017
exact_source: GSE15330_2825_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7019
exact_source: GSE15330_2831_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymphoid-primed multipotent progenitors versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7020
exact_source: GSE15330_2825_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7022
exact_source: GSE15330_2826_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7025
exact_source: GSE15330_2826_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7028
exact_source: GSE15330_2830_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in granulo-monocyte progenitors: wildtype versus IKZF1 [GeneID=10320] knockout.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7031
exact_source: GSE15330_2831_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymphoid-primed multipotent progenitors versus megakaryo-erythrocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7033
exact_source: GSE15330_2839_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: megakaryo-erythrocyte progenitors versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7035
exact_source: GSE15330_2824_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus lymphoid-primed multipotent progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7037
exact_source: GSE15330_2828_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymphoid-primed multipotent progenitors: wildtype versus IKZF1 [GeneID=10320] knockout.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7039
exact_source: GSE15330_2829_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in megakaryo-erythrocyte progenitors: wildtype versus IKZF1 [GeneID=10320] knockout.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7043
exact_source: GSE15330_2839_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: megakaryo-erythrocyte progenitors versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7044
exact_source: GSE15330_2829_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in megakaryo-erythrocyte progenitors: wildtype versus IKZF1 [GeneID=10320] knockout.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7046
exact_source: GSE15330_2835_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: lymphoid-primed multipotent progenitors versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7049
exact_source: GSE15330_2835_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IKZF1 [GeneID=10320] knockout: lymphoid-primed multipotent progenitors versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7050
exact_source: GSE15330_2824_200_UP
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IKZF1 [GeneID=10320] knockout: hematopoietic stem cells versus lymphoid-primed multipotent progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7058
exact_source: GSE15330_2828_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymphoid-primed multipotent progenitors: wildtype versus IKZF1 [GeneID=10320] knockout.

description_full:
[cell repeats an earlier one in this file: 585 characters]


systematic_name: M7059
exact_source: GSE15330_2819_200_DN
source_species_code: MM
GEO_id: GSE15330
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymphoid-primed multipotent progenitors versus granulo-monocyte progenitors.

description_full:
[cell repeats an earlier one in this file: 585 characters]


description_brief: Genes up-regulated in NK cells: low dose versus high dose of IL2 [GeneID=3558].
systematic_name: M7064
exact_source: GSE12198_3191_200_UP
source_species_code: HS
GEO_id: GSE12198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Transcriptional profiling of NKAES-derived NK cells after 7 days of culture compared to primary human NK cells and NK cells stimulated by low or high dose IL2 after 7 days of culture.


systematic_name: M7075
exact_source: GSE14908_3607_200_DN
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from atopic patients: resting versus stimulated with allergen (house dust mite).

description_full:
  The aim of this study was to employ a systems-level analysis to elucidate gene expression networks operating in the CD4 T-cell responses which underpin human atopic disease.


systematic_name: M7077
exact_source: GSE14908_3607_200_UP
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from atopic patients: resting versus stimulated with allergen (house dust mite).

description_full:
  The aim of this study was to employ a systems-level analysis to elucidate gene expression networks operating in the CD4 T-cell responses which underpin human atopic disease.


systematic_name: M7080
exact_source: GSE14908_3608_200_DN
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from non-atopic donors: resting versus stimulated with allergen (house dust mite).

description_full:
  The aim of this study was to employ a systems-level analysis to elucidate gene expression networks operating in the CD4 T-cell responses which underpin human atopic disease.


systematic_name: M7086
exact_source: GSE14908_3608_200_UP
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from non-atopic donors: resting versus stimulated with allergen (house dust mite).

description_full:
[cell repeats an earlier one in this file: 173 characters]


systematic_name: M7091
exact_source: GSE14908_3610_200_UP
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells stimulated with allergen (house dust mite): atopy versus healthy.

description_full:
[cell repeats an earlier one in this file: 173 characters]


systematic_name: M7097
exact_source: GSE14908_3610_200_DN
source_species_code: HS
GEO_id: GSE14908
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells stimulated with allergen (house dust mite): atopy versus healthy.

description_full:
[cell repeats an earlier one in this file: 173 characters]


description_brief: Genes down-regulated in neutrophils treated with CSF2 [GeneID=1437] versus control.
systematic_name: M7099
exact_source: GSE15139_2742_200_DN
source_species_code: HS
GEO_id: GSE15139
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The objective of this study was to compare the transcriptional repertoire of mature human neutrophils before and after GM-CSF treatment by using oligonucleotide microarrays. Leukotriene B4 (LTB4) is an important pro-inflammatory lipid mediator generated by neutrophils upon activation. Granulocyte/macrophage colony-stimulating factor (GM-CSF) stimulation is known to enhance agonist-mediated LTB4 production of neutrophils within minutes, a process called “priming”. Here, we demonstrate that GM-CSF also limits the production of LTB4 by neutrophils via a transcriptional mechanism at later time points. We identified hematopoietic specific Ras homologous (RhoH)/translocation three four (TTF), which was induced following GM-CSF stimulation in neutrophils, as a key regulator in this process. Neutrophils derived from RhoH/TTF-deficient (Rhoh-/-) mice demonstrated increased LTB4 production upon activation compared with normal mouse neutrophils. Moreover, neutrophils from cystic fibrosis patients expressed enhanced levels of RhoH/TTF and generated less LTB4 upon activation compared with normal human neutrophils. Taken together, these data suggest that RhoH/TTF represents an inducible feedback inhibitor in neutrophils that is involved in the limitation of innate immune responses.


description_brief: Genes down-regulated in centroblasts versus centrocytes.
systematic_name: M7101
exact_source: GSE15271_3464_200_DN
source_species_code: HS
GEO_id: GSE15271
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Functional discrimination between normal centroblast and centrocyte obtained from human inflamed tonsils after cell sorting. We used microarrays to detail the segregation between these two B cell subsets


systematic_name: M7105
exact_source: GSE15624_2677_200_UP
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with halofuginone [PubChem=400772]: 3h versus 6h.

description_full:
  T cell differentiation to the Th17 effector subset requires stimulation through the T cell and co-stimulatory receptors, together with cytokine stimulation by TGFb and IL-6. The small molecule halofuginone (HF) inhibits Th17 cell development and induces a pattern of stress-regulated gene expression that mimics amino acid starvation. We used global transcript profiling to ask how halofuginone modulates gene expression induced during T cell activaiton and Th17 differentiation


systematic_name: M7106
exact_source: GSE15624_2676_200_DN
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: control versus treated with halofuginone [PubChem=400772] for 6h.

description_full:
  T cell differentiation to the Th17 effector subset requires stimulation through the T cell and co-stimulatory receptors, together with cytokine stimulation by TGFb and IL-6. The small molecule halofuginone (HF) inhibits Th17 cell development and induces a pattern of stress-regulated gene expression that mimics amino acid starvation. We used global transcript profiling to ask how halofuginone modulates gene expression induced during T cell activaiton and Th17 differentiation


systematic_name: M7109
exact_source: GSE15624_2677_200_DN
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with halofuginone [PubChem=400772]: 3h versus 6h.

description_full:
  T cell differentiation to the Th17 effector subset requires stimulation through the T cell and co-stimulatory receptors, together with cytokine stimulation by TGFb and IL-6. The small molecule halofuginone (HF) inhibits Th17 cell development and induces a pattern of stress-regulated gene expression that mimics amino acid starvation. We used global transcript profiling to ask how halofuginone modulates gene expression induced during T cell activaiton and Th17 differentiation


systematic_name: M7111
exact_source: GSE15624_2676_200_UP
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: control versus treated with halofuginone [PubChem=400772] for 6h.

description_full:
[cell repeats an earlier one in this file: 478 characters]


systematic_name: M7115
exact_source: GSE15624_2675_200_DN
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: control versus treated with halofuginone [PubChem=400772] for 3h.

description_full:
[cell repeats an earlier one in this file: 478 characters]


systematic_name: M7116
exact_source: GSE15624_2675_200_UP
source_species_code: MM
GEO_id: GSE15624
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: control versus treated with halofuginone [PubChem=400772] for 3h.

description_full:
[cell repeats an earlier one in this file: 478 characters]


description_brief: Genes up-regulated in peripheral blood monocytes (PMBC): healthy versus Gram negative sepsis.
systematic_name: M7118
exact_source: GSE9960_3816_200_UP
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  To identify signature genes that help distinguish (1) sepsis from non-infectious causes of systemic inflammatory response syndrome, (2) between Gram-positive and Gram-negative sepsis.


systematic_name: M7128
exact_source: GSE9960_3820_200_UP
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in peripheral blood monocytes (PMBC): Gram negative sepsis versus Gram positive sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7129
exact_source: GSE9960_3820_200_DN
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in peripheral blood monocytes (PMBC): Gram negative sepsis versus Gram positive sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7130
exact_source: GSE9960_3821_200_UP
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in peripheral blood monocytes (PMBC): Gram negative sepsis versus mixed infection sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7131
exact_source: GSE9960_3821_200_DN
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in peripheral blood monocytes (PMBC): Gram negative sepsis versus mixed infection sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7132
exact_source: GSE9960_3822_200_UP
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in peripheral blood monocytes (PMBC): Gram positive sepsis versus mixed infection sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7133
exact_source: GSE9960_3822_200_DN
source_species_code: HS
GEO_id: GSE9960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in peripheral blood monocytes (PMBC): Gram positive sepsis versus mixed infection sepsis.

description_full:
[cell repeats an earlier one in this file: 183 characters]


systematic_name: M7134
exact_source: GSE12392_2737_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in splenic dendritic cells from IFNB1 [GeneID=3456] knockout mice: CD8A+ [GeneID=925] versus CD8A- [GeneID=925] populations.

description_full:
  Type I Interferons encompasses a large family of closely related cytokines comprising of at least 13 IFN-α isotypes and single IFN-β. Both IFN-α and IFN-β exert their activity through a common receptor IFNAR. Type I Interferons have broad regulatory effects and various subtypes of dendritic cells are influenced by this cytokines. In our study we asked question whether the low, constitutive levels of type I Interferons produced under steady state conditions are important for proper function of splenic conventional dendritic cells.


systematic_name: M7135
exact_source: GSE12392_2735_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype splenic dendritic cells: CD8A+ [GeneID=925] versus CD8A- [GeneID=925].

description_full:
  Type I Interferons encompasses a large family of closely related cytokines comprising of at least 13 IFN-α isotypes and single IFN-β. Both IFN-α and IFN-β exert their activity through a common receptor IFNAR. Type I Interferons have broad regulatory effects and various subtypes of dendritic cells are influenced by this cytokines. In our study we asked question whether the low, constitutive levels of type I Interferons produced under steady state conditions are important for proper function of splenic conventional dendritic cells.


systematic_name: M7136
exact_source: GSE12392_2741_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8A- [GeneID=925] splenic dendritic cells: IFNAR1 [GeneID=3454] knockout versus IFNB1 [GeneID=3456] knockout.

description_full:
  Type I Interferons encompasses a large family of closely related cytokines comprising of at least 13 IFN-α isotypes and single IFN-β. Both IFN-α and IFN-β exert their activity through a common receptor IFNAR. Type I Interferons have broad regulatory effects and various subtypes of dendritic cells are influenced by this cytokines. In our study we asked question whether the low, constitutive levels of type I Interferons produced under steady state conditions are important for proper function of splenic conventional dendritic cells.


systematic_name: M7138
exact_source: GSE12392_2737_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in splenic dendritic cells from IFNB1 [GeneID=3456] knockout mice: CD8A+ [GeneID=925] versus CD8A- [GeneID=925] populations.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7139
exact_source: GSE12392_2739_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8A- [GeneID=925] splenic dendritic cells: wildtype versus IFNAR1 [GeneID=3454] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7142
exact_source: GSE12392_2741_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8A- [GeneID=925] splenic dendritic cells: IFNAR1 [GeneID=3454] knockout versus IFNB1 [GeneID=3456] knockout.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7143
exact_source: GSE12392_2735_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype splenic dendritic cells: CD8A+ [GeneID=925] versus CD8A- [GeneID=925].

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7144
exact_source: GSE12392_2738_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8A+ [GeneID=925] splenic dendritic cells: wildtype versus IFNB1 [GeneID=3456] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7147
exact_source: GSE12392_2739_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8A- [GeneID=925] splenic dendritic cells: wildtype versus IFNAR1 [GeneID=3454] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7148
exact_source: GSE12392_2740_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8A- [GeneID=925] splenic dendritic cells: wildtype versus IFNB1 [GeneID=3456] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7150
exact_source: GSE12392_2740_200_DN
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8A- [GeneID=925] splenic dendritic cells: wildtype versus IFNB1 [GeneID=3456] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


systematic_name: M7152
exact_source: GSE12392_2738_200_UP
source_species_code: MM
GEO_id: GSE12392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8A+ [GeneID=925] splenic dendritic cells: wildtype versus IFNB1 [GeneID=3456] knockout mice.

description_full:
[cell repeats an earlier one in this file: 535 characters]


description_brief: Genes up-regulated in CD4 [GeneID=920] T cells versus follicular helper CD4 [GeneID=920] T cells.
systematic_name: M7153
exact_source: GSE16697_2667_200_UP
source_species_code: MM
GEO_id: GSE16697
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) follicular helper CD4 T cells (CXCR5high),versus non-follicular helper CD4 T cells (CXCR5low), eight days after viral infection. A paper including data analysis of these experiments has been accepted for publication (Robert J. Johnston et al. Bcl6 and Blimp-1 are reciprocal and antagonistic regulators of follicular helper CD4 T cell differentiation).


description_brief: Genes up-regulated in CD4 [GeneID=920] T cells: control versus treated with HDAC inhibitors for 2h.
systematic_name: M7156
exact_source: GSE15735_2248_200_UP
source_species_code: HS
GEO_id: GSE15735
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Histone acetyltransferases (HATs) and deacetylases (HDACs) function antagonistically to control histone acetylation. As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. We describe here genome-wide mapping of HATs and HDACs binding on chromatin and ﬁnd that both are found at active genes with acetylated histones. Our data provide evidence that HATs and HDACs are both targeted to transcribed regions of active genes by phosphorylated RNA Pol II. Furthermore, the majority of HDACs in the human genome function to reset chromatin by removing acetylation at active genes. Inactive genes that are primed by MLL-mediated histone H3K4 methylation are subject to a dynamic cycle of acetylation and deacetylation by transient HAT/HDAC binding, preventing Pol II from binding to these genes but poising them for future activation. Silent genes without any H3K4 methylation signal show no evidence of being bound by HDACs.


systematic_name: M7157
exact_source: GSE15735_2249_200_DN
source_species_code: HS
GEO_id: GSE15735
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: control versus treated with HDAC inhibitors for 12h.

description_full:
  Histone acetyltransferases (HATs) and deacetylases (HDACs) function antagonistically to control histone acetylation. As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. We describe here genome-wide mapping of HATs and HDACs binding on chromatin and ﬁnd that both are found at active genes with acetylated histones. Our data provide evidence that HATs and HDACs are both targeted to transcribed regions of active genes by phosphorylated RNA Pol II. Furthermore, the majority of HDACs in the human genome function to reset chromatin by removing acetylation at active genes. Inactive genes that are primed by MLL-mediated histone H3K4 methylation are subject to a dynamic cycle of acetylation and deacetylation by transient HAT/HDAC binding, preventing Pol II from binding to these genes but poising them for future activation. Silent genes without any H3K4 methylation signal show no evidence of being bound by HDACs.


systematic_name: M7161
exact_source: GSE15735_2248_200_DN
source_species_code: HS
GEO_id: GSE15735
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: control versus treated with HDAC inhibitors for 2h.

description_full:
[cell repeats an earlier one in this file: 991 characters]


systematic_name: M7163
exact_source: GSE15735_2249_200_UP
source_species_code: HS
GEO_id: GSE15735
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: control versus treated with HDAC inhibitors for 12h.

description_full:
[cell repeats an earlier one in this file: 991 characters]


description_brief: Genes down-regulated in memory CD8 T cells: wildtype wt versus ZBTB7B [GeneID=51043] knockout.
systematic_name: M7164
exact_source: GSE17812_2733_200_DN
source_species_code: MM
GEO_id: GSE17812
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  We noticed that ThPOK repression is readily abrogated upon in vitro TCR stimulation of peripheral CD8 T cells. This observation prompted us to investigate a role of ThPOK in the CD8 T cell response to an acute viral infection. We observed that clonal expansion is significantly less in both primary and secondary CD8 T cell responses in the absence of functional ThPOK. To approach this mechanism, we carried out a microarray analysis for comparison of gene expression between ThPOKhd/hd and ThPOKwt/wt P14 memory T cells.


systematic_name: M7168
exact_source: GSE17186_3139_200_UP
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in transitional B lymphocytes: CR2 [GeneID=1380] low versus CR2 [GeneID=1380] high.

description_full:
  Goals/objectives: to identify various gene expression in B cell subsets derived from human PBMC and cord blood


systematic_name: M7172
exact_source: GSE17186_3141_200_UP
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes from cord blood: naïve versus transitional CR2 [GeneID=1380] high.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7174
exact_source: GSE17186_3139_200_DN
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in transitional B lymphocytes: CR2 [GeneID=1380] low versus CR2 [GeneID=1380] high.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7185
exact_source: GSE17186_3145_200_UP
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in transitional CR2 [GeneID=1380] high B lymphocytes versus those from cord blood.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7186
exact_source: GSE17186_3145_200_DN
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in transitional CR2 [GeneID=1380] high B lymphocytes versus those from cord blood.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7190
exact_source: GSE17186_3141_200_DN
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes from cord blood: naïve versus transitional CR2 [GeneID=1380] high.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7192
exact_source: GSE17186_3142_200_UP
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in transitional B lymphocytes from cord blood: CR2 [GeneID=1380] low versus CR2 [GeneID=1380] high.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7193
exact_source: GSE17186_3142_200_DN
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in transitional B lymphocytes from cord blood: CR2 [GeneID=1380] low versus CR2 [GeneID=1380] high.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7195
exact_source: GSE17186_3144_200_UP
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in transitional CR2 [GeneID=1380] low B lymphocytes versus those from cord blood.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7196
exact_source: GSE17186_3144_200_DN
source_species_code: HS
GEO_id: GSE17186
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in transitional CR2 [GeneID=1380] low B lymphocytes versus those from cord blood.

description_full:
[cell repeats an earlier one in this file: 110 characters]


systematic_name: M7207
exact_source: GSE18203_3834_200_UP
source_species_code: MM
GEO_id: GSE18203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in tumors established by injecting MC38 cells (colon cancer): control versus CpG oligodeoxynucleotide 1826.

description_full:
  To determine the effect on gene expression of intratumoral injection of the Toll-like receptor agonist CpG1826. MC38 colon cancer cells were injected subcutaneously into C57BL/6 mice and allowed to establish until ~40 mm2.


systematic_name: M7208
exact_source: GSE18203_3834_200_DN
source_species_code: MM
GEO_id: GSE18203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in tumors established by injecting MC38 cells (colon cancer): control versus CpG oligodeoxynucleotide 1826.

description_full:
  To determine the effect on gene expression of intratumoral injection of the Toll-like receptor agonist CpG1826. MC38 colon cancer cells were injected subcutaneously into C57BL/6 mice and allowed to establish until ~40 mm2.


description_brief: Genes down-regulated inmouse embryonic fibroblasts (MEF): control versus LPS and heat shock.
systematic_name: M7209
exact_source: GSE16266_3079_200_DN
source_species_code: MM
GEO_id: GSE16266
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  To clarify inflammatory genes whose expression is suppressed at high temperatures, we performed comprehensive analysis of gene expression by using a DNA microarray. Two independent primary cultures of mouse embryo fibroblasts (MEF1 and MEF2) were treated with LPS for 4 hours, or treated with LPS for 4 hours after the pretreatment with heat shock at 42˚C for 1 hour, and we identified 100 genes that undergo more than a 3-fold increase with LPS treatment. Remarkably, 86 genes (86%) underwent less than a 2-fold increase after combined treatments with heat shock and LPS in MEF1 and MEF2 cells.


description_brief: Genes up-regulated in T cells: control (0h) versus IL21 [GeneID=59067] treatment for 6h.
systematic_name: M7221
exact_source: GSE19198_2365_200_UP
source_species_code: MM
GEO_id: GSE19198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Interleukin-21 (IL-21) is a pleiotropic cytokine that induces expression of transcription factor BLIMP1 (encoded by Prdm1), which regulates plasma cell differentiation and T cell homeostasis. We identified an IL-21 response element downstream of Prdm1 that binds the transcription factors STAT3 and IRF4, which are required for optimal Prdm1 expression. Genome-wide ChIP-Seq mapping of STAT3- and IRF4-binding sites showed that most regions with IL-21-induced STAT3 binding also bound IRF4 in vivo, and furthermore, revealed that the noncanonical TTCnnnTAA GAS motif critical in Prdm1 was broadly used for STAT3 binding. Comparing genome-wide expression array data to binding sites revealed that most IL-21-regulated genes were associated with combined STAT3-IRF4 sites rather than pure STAT3 sites. Correspondingly, ChIP-Seq analysis of Irf4_/_ T cells showed greatly diminished STAT3 binding after IL-21 treatment, and Irf4_/_ mice showed impaired IL- 21-induced Tfh cell differentiation in vivo. These results reveal broad cooperative gene regulation by STAT3 and IRF4.


description_brief: Genes up-regulated in thymus cortical regions: subcapsular versus perimedullary.
systematic_name: M7235
exact_source: GSE18281_2548_200_UP
source_species_code: MM
GEO_id: GSE18281
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Interaction of hematopoietic progenitors with the thymic stromal microenvironment induces them to proliferate, adopt the T cell fate, and asymmetrically diverge into multiple T lineages. Progenitors at various developmental stages are stratified among different regions of the thymus, implying that the corresponding microenvironments differ from one another, and provide unique sets of signals to progenitors migrating between them. The nature of these differences remains undefined. Here we use novel physical and computational approaches to characterize these stromal subregions, distinguishing gene expression in microdissected tissues from that of their lymphoid constituents. Using this approach, we comprehensively map gene expression in functionally distinct stromal microenvironments, and identify clusters of genes that define each region. Quite unexpectedly, we find that the central cortex lacks distinctive features of its own, and instead appears to function by sequestering unique microenvironments found at the cortical extremities, and modulating the relative proximity of progenitors moving between them.


description_brief: Genes up-regulated in bone marrow-derived macrophages: control versus Listeria infected.
systematic_name: M7264
exact_source: GSE19374_2404_200_UP
source_species_code: MM
GEO_id: GSE19374
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Macrophages phagocytose bacteria. Certain pathogenic bacteria access and replicate within the cytosol of infected macrophages and induce changes in macrophage gene expression by triggering of innate immune receptors and/or the effects of bacterial virulence factors. We used microarray analysis to identify changes in macrophage gene expression following infection with Listeria monocytogenes.


systematic_name: M7266
exact_source: GSE19923_2930_200_DN
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes: TCF3 [GeneID=6929] knockout versus TCF12 [GeneID=6938] knockout.

description_full:
  We wanted to test the role of mammalian E proteins E2A and HEB in the development of T cells. Using a conditional deletion system in which these proteins are deleted at the DP stage of T cell development, we compared DP thymocytes deficient for E2A, HEB or both to wild-type thymocytes


systematic_name: M7269
exact_source: GSE19923_2927_200_DN
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes: wildtype versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7270
exact_source: GSE19923_2929_200_UP
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes: TCF12 [GeneID=6939] knockout versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7271
exact_source: GSE19923_2929_200_DN
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes: TCF12 [GeneID=6939] knockout versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7273
exact_source: GSE19923_2927_200_UP
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes: wildtype versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7274
exact_source: GSE19923_2930_200_UP
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes: TCF3 [GeneID=6929] knockout versus TCF12 [GeneID=6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7275
exact_source: GSE19923_2928_200_UP
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positve thymocyte: TCF3 [GeneID=6929] knockout versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7276
exact_source: GSE19923_2928_200_DN
source_species_code: MM
GEO_id: GSE19923
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positve thymocyte: TCF3 [GeneID=6929] knockout versus TCF3 and TCF12 [GeneID=6929;6938] knockout.

description_full:
[cell repeats an earlier one in this file: 285 characters]


systematic_name: M7280
exact_source: GSE19772_3042_200_DN
source_species_code: HS
GEO_id: GSE19772
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes pre-treated with Ly294002 [PubChem=3973]: control versus HCMV infection.

description_full:
  Human cytomegalovirus (HCMV) induces pro-inflammatory monocytes following infection and we have evidence that phosphatidylinositol 3-kinase [PI(3)K] is a key mediator in this activation. To begin to address how this signalling pathway is responsible for the functional changes in infected monocytes, we examined the role this pathway played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes were regulated in a PI(3)K-dependent manner, identifying this pathway as a key cellular control point in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.


systematic_name: M7283
exact_source: GSE19772_3043_200_UP
source_species_code: HS
GEO_id: GSE19772
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes after HCMV infection: untreated versus pre-treated with Ly294002 [PubChem=3973].

description_full:
  Human cytomegalovirus (HCMV) induces pro-inflammatory monocytes following infection and we have evidence that phosphatidylinositol 3-kinase [PI(3)K] is a key mediator in this activation. To begin to address how this signalling pathway is responsible for the functional changes in infected monocytes, we examined the role this pathway played in the transcriptome of infected monocytes. Global transcriptional profiling using cDNA microarrays revealed a significant number of genes were regulated in a PI(3)K-dependent manner, identifying this pathway as a key cellular control point in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.


systematic_name: M7286
exact_source: GSE19772_3043_200_DN
source_species_code: HS
GEO_id: GSE19772
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes after HCMV infection: untreated versus pre-treated with Ly294002 [PubChem=3973].

description_full:
[cell repeats an earlier one in this file: 677 characters]


systematic_name: M7288
exact_source: GSE19772_3042_200_UP
source_species_code: HS
GEO_id: GSE19772
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes pre-treated with Ly294002 [PubChem=3973]: control versus HCMV infection.

description_full:
[cell repeats an earlier one in this file: 677 characters]


description_brief: Genes down-regulated in lymphocytes treated with medium for 24h: T conv versus T reg cells.
systematic_name: M7289
exact_source: GSE18893_1274_200_DN
source_species_code: HS
GEO_id: GSE18893
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Here we show that tumor necrosis factor (TNF) induced in human T-regulatory cells (Treg), as compared to conventional T cells (Tcon), a transcription program highly enriched for typical NF-κB target genes, such as: the cytokines LTA and TNF; the TNF-receptor super family members FAS, 4-1BB and OX-40; various anti-apoptotic genes; and other important immune-response genes. As an initial approach to examine the cellular program induced by TNF in Tregs versus Tcon cells, we employed microarray gene expression analysis at 2 and 24 hrs following TNF treatment.


systematic_name: M7291
exact_source: GSE18893_1280_200_DN
source_species_code: HS
GEO_id: GSE18893
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymphocytes treated with TNF [GeneID=7124] for 24h: T conv versus T reg cells.

description_full:
  Here we show that tumor necrosis factor (TNF) induced in human T-regulatory cells (Treg), as compared to conventional T cells (Tcon), a transcription program highly enriched for typical NF-κB target genes, such as: the cytokines LTA and TNF; the TNF-receptor super family members FAS, 4-1BB and OX-40; various anti-apoptotic genes; and other important immune-response genes. As an initial approach to examine the cellular program induced by TNF in Tregs versus Tcon cells, we employed microarray gene expression analysis at 2 and 24 hrs following TNF treatment.


systematic_name: M7306
exact_source: GSE18893_1279_200_DN
source_species_code: HS
GEO_id: GSE18893
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymphocytes treated with TNF [GeneID=7124] for 2h: T conv versus T reg cells.

description_full:
[cell repeats an earlier one in this file: 561 characters]


systematic_name: M7308
exact_source: GSE18893_1280_200_UP
source_species_code: HS
GEO_id: GSE18893
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymphocytes treated with TNF [GeneID=7124] for 24h: T conv versus T reg cells.

description_full:
[cell repeats an earlier one in this file: 561 characters]


systematic_name: M7310
exact_source: GSE19888_3592_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1.

description_full:
  We demonstrate that the G protein Gi3 is the cellular target of the adenosine A3 receptor (A3R). By using a cell permeable peptide comprising the C-terminal end of Gαi3 fused to an importation sequence (ALL1) as a selective inhibitor of Gi3 signaling, we show that by coupling to Gi3, the A3R stimulates multiple signaling pathways in human mast cells, leading to upregulation of cytokines, chemokines and growth factors.Following contact with activated T cell membranes, endogenous adenosine binds to and activates the A3R, resulting in Gi3-mediated signaling. Specifically, the majority of ERK1/2 signaling initiated by contact with activated T cell membranes, is mediated by Gi3, giving rise to ALL1-inhibitable cellular responses. These results unveil the physiological GPCR that couples to Gi3 and establish the important role played by this G-protein in inflammatory conditions that involve adenosine-activated mast cells. We used microarrays to detail the effect of ALL1 on gene expression of HMC-1 cells activated directly by the A3 receptor, or by contact with activated T cell membranes.


systematic_name: M7311
exact_source: GSE19888_3592_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1.

description_full:
  We demonstrate that the G protein Gi3 is the cellular target of the adenosine A3 receptor (A3R). By using a cell permeable peptide comprising the C-terminal end of Gαi3 fused to an importation sequence (ALL1) as a selective inhibitor of Gi3 signaling, we show that by coupling to Gi3, the A3R stimulates multiple signaling pathways in human mast cells, leading to upregulation of cytokines, chemokines and growth factors.Following contact with activated T cell membranes, endogenous adenosine binds to and activates the A3R, resulting in Gi3-mediated signaling. Specifically, the majority of ERK1/2 signaling initiated by contact with activated T cell membranes, is mediated by Gi3, giving rise to ALL1-inhibitable cellular responses. These results unveil the physiological GPCR that couples to Gi3 and establish the important role played by this G-protein in inflammatory conditions that involve adenosine-activated mast cells. We used microarrays to detail the effect of ALL1 on gene expression of HMC-1 cells activated directly by the A3 receptor, or by contact with activated T cell membranes.


systematic_name: M7313
exact_source: GSE19888_3605_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells incubated with the peptide ALL1 followed by treatment with: Cl-IB-MECA [PubChem=3035850] versus T cell membranes.

description_full:
  We demonstrate that the G protein Gi3 is the cellular target of the adenosine A3 receptor (A3R). By using a cell permeable peptide comprising the C-terminal end of Gαi3 fused to an importation sequence (ALL1) as a selective inhibitor of Gi3 signaling, we show that by coupling to Gi3, the A3R stimulates multiple signaling pathways in human mast cells, leading to upregulation of cytokines, chemokines and growth factors.Following contact with activated T cell membranes, endogenous adenosine binds to and activates the A3R, resulting in Gi3-mediated signaling. Specifically, the majority of ERK1/2 signaling initiated by contact with activated T cell membranes, is mediated by Gi3, giving rise to ALL1-inhibitable cellular responses. These results unveil the physiological GPCR that couples to Gi3 and establish the important role played by this G-protein in inflammatory conditions that involve adenosine-activated mast cells. We used microarrays to detail the effect of ALL1 on gene expression of HMC-1 cells activated directly by the A3 receptor, or by contact with activated T cell membranes.


systematic_name: M7316
exact_source: GSE19888_3601_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus incubated with the ALL1 peptide followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7317
exact_source: GSE19888_3602_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7318
exact_source: GSE19888_3603_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus incubated with the peptide ALL1 followed by stimulation with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7319
exact_source: GSE19888_3603_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus incubated with the peptide ALL1 followed by stimulation with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7320
exact_source: GSE19888_3604_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: incubated with the peptide ALL1 and then treated with Cl-IB-MECA [PubChem=3035850] versus stimulation by T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7321
exact_source: GSE19888_3604_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: incubated with the peptide ALL1 and then treated with Cl-IB-MECA [PubChem=3035850] versus stimulation by T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7322
exact_source: GSE19888_3598_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells incubated the peptide ALL1 versus those followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7323
exact_source: GSE19888_3598_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells incubated the peptide ALL1 versus those followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7324
exact_source: GSE19888_3599_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: incubated with the peptide ALL1 versus stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7329
exact_source: GSE19888_3594_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1 followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7332
exact_source: GSE19888_3601_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus incubated with the ALL1 peptide followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7333
exact_source: GSE19888_3602_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: Cl-IB-MECA [PubChem=3035850] versus T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7334
exact_source: GSE19888_3595_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: untreated versus stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7335
exact_source: GSE19888_3596_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1 followed by stimulation with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7336
exact_source: GSE19888_3596_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1 followed by stimulation with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7340
exact_source: GSE19888_3597_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells incubated with: the peptide ALL1 versus Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7341
exact_source: GSE19888_3597_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells incubated with: the peptide ALL1 versus Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7342
exact_source: GSE19888_3600_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells incubated with the peptide ALL1 versus those then stimulated by T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7345
exact_source: GSE19888_3600_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells incubated with the peptide ALL1 versus those then stimulated by T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7347
exact_source: GSE19888_3606_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: stimulated with T cell membranes versus incubated with the peptide ALL1 and then stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7350
exact_source: GSE19888_3599_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: incubated with the peptide ALL1 versus stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7351
exact_source: GSE19888_3594_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells: untreated versus incubated with the peptide ALL1 followed by treatment with Cl-IB-MECA [PubChem=3035850].

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7352
exact_source: GSE19888_3595_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: untreated versus stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7353
exact_source: GSE19888_3605_200_DN
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in HMC-1 (mast leukemia) cells incubated with the peptide ALL1 followed by treatment with: Cl-IB-MECA [PubChem=3035850] versus T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


systematic_name: M7354
exact_source: GSE19888_3606_200_UP
source_species_code: HS
GEO_id: GSE19888
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in HMC-1 (mast leukemia) cells: stimulated with T cell membranes versus incubated with the peptide ALL1 and then stimulated with T cell membranes.

description_full:
[cell repeats an earlier one in this file: 1097 characters]


description_brief: Genes down-regulated in nuocytes: control versus treated with IL7 and IL33 [GeneID=3574;90865].
systematic_name: M7356
exact_source: GSE25890_2642_200_DN
source_species_code: MM
GEO_id: GSE25890
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Nuocytes are a recently described cell that responds to both IL-25 and IL-33 and produce high levels of IL-13 and IL-5


description_brief: Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): control versus IL-12.
systematic_name: M7361
exact_source: GSE20198_2508_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The aim of this study was to identify genes regulated by IL-12, IL-18 and IFN-alpha during early differentiation of human Th1 cells


systematic_name: M7366
exact_source: GSE20198_2510_200_UP
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the activated CD4 [GeneID=920] T cells (48h): control versus interferon alpha.

description_full:
  The aim of this study was to identify genes regulated by IL-12, IL-18 and IFN-alpha during early differentiation of human Th1 cells


systematic_name: M7369
exact_source: GSE20198_2513_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): IL-12 and IL18 [GeneID=3606] versus interferon alpha.

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7370
exact_source: GSE20198_2513_200_UP
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the activated CD4 [GeneID=920] T cells (48h): IL-12 and IL18 [GeneID=3606] versus interferon alpha.

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7372
exact_source: GSE20198_2511_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): IL-12 versus IL-12 and IL18 [GeneID=3606].

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7373
exact_source: GSE20198_2509_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): control versus IL-12 and IL18 [GeneID=3606].

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7374
exact_source: GSE20198_2512_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): IL-12 versus interferon alpha.

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7376
exact_source: GSE20198_2510_200_DN
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the activated CD4 [GeneID=920] T cells (48h): control versus interferon alpha.

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7379
exact_source: GSE20198_2509_200_UP
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the activated CD4 [GeneID=920] T cells (48h): control versus IL-12 and IL18 [GeneID=3606].

description_full:
[cell repeats an earlier one in this file: 131 characters]


systematic_name: M7380
exact_source: GSE20198_2511_200_UP
source_species_code: HS
GEO_id: GSE20198
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the activated CD4 [GeneID=920] T cells (48h): IL-12 versus IL-12 and IL18 [GeneID=3606].

description_full:
[cell repeats an earlier one in this file: 131 characters]


description_brief: Genes down-regulated in monocyte derived macrophages: CSF1 [GeneID=1435] versus PF4 [GeneID=5196].
systematic_name: M7382
exact_source: GSE20484_2502_200_DN
source_species_code: HS
GEO_id: GSE20484
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Human blood monocytes were differentiated over six days with either 100 ng/ml M-CSF or 1 umol/l CXCL4 In atherosclerotic arteries, blood monocytes differentiate to macrophages in the presence of growth factors like macrophage colony-stimulation factor (MCSF) and chemokines like platelet factor 4 (CXCL4). To compare the gene expression signature of CXCL4-induced macrophages with MCSF-induced macrophages or macrophages polarized with IFN-γ/LPS (M1) or IL-4 (M2), we cultured primary human peripheral blood monocytes for six days. mRNA expression was measured by Affymetrix gene chips and differences were analyzed by Local Pooled Error test, Profile of Complex Functionality and Gene Set Enrichment Analysis. 375 genes were differentially expressed between MCSF- and CXCL4-induced macrophages, 206 of them overexpressed in CXCL4 macrophages coding for genes implicated in the inflammatory/immune response, antigen processing/presentation, and lipid metabolism. CXCL4-induced macrophages overexpressed some M1 and M2 genes and the corresponding cytokines at the protein level, however, their transcriptome clustered with neither M1 nor M2 transcriptomes. They almost completely lost the ability to phagocytose zymosan beads. Genes linked to atherosclerosis were not consistently up- or downregulated. Scavenger receptors showed lower and cholesterol efflux transporters higher expression in CXCL4- than MCSF-induced macrophages, resulting in lower LDL content. We conclude that CXCL4 induces a unique macrophage transcriptome distinct from known macrophage types, defining a new macrophage differentiation that we propose to call M4.


description_brief: Genes up-regulated in lung dendritic cells: CD103+ [GeneID=3682] versus CD11b [GeneID=3684] high.
systematic_name: M7389
exact_source: GSE17322_2402_200_UP
source_species_code: MM
GEO_id: GSE17322
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Mouse lung CD11c+ dendritic cells are composed of 2 major DC subsets, the CD103+CD11b-low/intermediate DC (CD103+ DC) and the CD11b-highCD103- DC (CD11b-high DC). These 2 subsets are functionally distinct. Comparison of their functions showed CD103+ DC Microarray analysis was performed to compare the gene expression profiles of the 2 lung DC subsets in naïve mice.


systematic_name: M7390
exact_source: GSE17322_2402_200_DN
source_species_code: MM
GEO_id: GSE17322
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lungh dendritic cell : CD103+ [GeneID=3682] versus CD11b [GeneID=3684] high.

description_full:
  Mouse lung CD11c+ dendritic cells are composed of 2 major DC subsets, the CD103+CD11b-low/intermediate DC (CD103+ DC) and the CD11b-highCD103- DC (CD11b-high DC). These 2 subsets are functionally distinct. Comparison of their functions showed CD103+ DC Microarray analysis was performed to compare the gene expression profiles of the 2 lung DC subsets in naïve mice.


description_brief: Genes down-regulated in T reg cells: wildtype versus FOXO1 and FOXO3 [GeneID=2308;2309].
systematic_name: M7394
exact_source: GSE21678_2640_200_DN
source_species_code: MM
GEO_id: GSE21678
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Identification of Foxos target genes in Treg cells. Foxo1and Foxo3 are transcription factors of Foxo family. CD4+Foxp3+ Treg cells isolated from wild-type and Foxo1/3-deficient mice were analyzed by global gene expression profiling. Results indicate Foxos regulate expression of a subset of Treg cell signature genes and genes in control of T cell homeostasis, signaling and metabolism.


description_brief: Genes up-regulated in the neuron cell line: immature versus mature.
systematic_name: M7397
exact_source: GSE16450_3398_200_UP
source_species_code: HS
GEO_id: GSE16450
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Human neuronal differentiation alters responsiveness to innate immune stimuli and virus infections. We used microarrays to examine the transcriptional responses of the human BE(2)-C neuroblastoma cell line to retinoic acid-induced differentiation and type I IFN stimulation.


systematic_name: M7408
exact_source: GSE16451_3457_200_DN
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in neuron cell line infected with western equine encephalitis virus: immature versus mature cells.

description_full:
  Human neuronal differentiation alters responsiveness to innate immune stimuli and virus infections. We used microarrays to examine the transcriptional responses of the human BE(2)-C neuroblastoma cell line to infection with western equine encephalitis virus (WEEV).


systematic_name: M7413
exact_source: GSE16451_3457_200_UP
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in neuron cell line infected with western equine encephalitis virus: immature versus mature cells.

description_full:
  Human neuronal differentiation alters responsiveness to innate immune stimuli and virus infections. We used microarrays to examine the transcriptional responses of the human BE(2)-C neuroblastoma cell line to infection with western equine encephalitis virus (WEEV).


systematic_name: M7414
exact_source: GSE16450_3399_200_UP
source_species_code: HS
GEO_id: GSE16450
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in neuron cell line treated with interferon alpha for 6h: immature versus mature.

description_full:
[cell repeats an earlier one in this file: 274 characters]


systematic_name: M7415
exact_source: GSE16450_3399_200_DN
source_species_code: HS
GEO_id: GSE16450
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in neuron cell line treated with interferon alpha for 6h: immature versus mature.

description_full:
[cell repeats an earlier one in this file: 274 characters]


systematic_name: M7418
exact_source: GSE16450_3400_200_DN
source_species_code: HS
GEO_id: GSE16450
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in neuron cell line treated with interferon alpha for 12h: immature versus mature.

description_full:
[cell repeats an earlier one in this file: 274 characters]


systematic_name: M7424
exact_source: GSE16451_3455_200_UP
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the mature neuron cell line: control versus infected with western equine encephalitis virus.

description_full:
  Human neuronal differentiation alters responsiveness to innate immune stimuli and virus infections. We used microarrays to examine the transcriptional responses of the human BE(2)-C neuroblastoma cell line to infection with western equine encephalitis virus (WEEV).


systematic_name: M7426
exact_source: GSE16451_3455_200_DN
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the mature neuron cell line: control versus infected with western equine encephalitis virus.

description_full:
[cell repeats an earlier one in this file: 265 characters]


systematic_name: M7427
exact_source: GSE16451_3454_200_UP
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the immature neuron cell line: control versus infected with western equine encephalitis viruss.

description_full:
[cell repeats an earlier one in this file: 265 characters]


systematic_name: M7428
exact_source: GSE16451_3454_200_DN
source_species_code: HS
GEO_id: GSE16451
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the immature neuron cell line: control versus infected with western equine encephalitis viruss.

description_full:
[cell repeats an earlier one in this file: 265 characters]


systematic_name: M7430
exact_source: GSE16450_3400_200_UP
source_species_code: HS
GEO_id: GSE16450
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in neuron cell line treated with interferon alpha for 12h: immature versus mature.

description_full:
[cell repeats an earlier one in this file: 274 characters]


systematic_name: M7431
exact_source: GSE21670_2386_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus TGF beta and IL6 [GeneID=3569].

description_full:
  STAT3, an essential transcription factor with pleiotropic functions, plays critical roles in the pathogenesis of autoimmunity. Despite recent data linking STAT3 with inflammatory bowel disease, exactly how it contributes to chronic intestinal inflammation is not known. Using a T cell transfer model of colitis we found that STAT3 expression in T cells was essential for the induction of both colitis and systemic inflammation. STAT3 was critical in modulating the balance of T helper 17 (Th17) and regulatory T (Treg) cells, as well as in promoting CD4+ T cell proliferation. We used chromatin immunoprecipitation and massive parallel sequencing (ChIP-Seq) to define the genome-wide targets of STAT3 in CD4+ T cells. We found that STAT3 bound to multiple genes involved in Th17 cell differentiation, cell activation, proliferation and survival, regulating both expression and epigenetic modifications. Thus, STAT3 orchestrates multiple critical aspects of T cell function in inflammation and homeostasis.


systematic_name: M7432
exact_source: GSE21670_2375_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: TGF beta versus IL6 [GeneID=3569].

description_full:
  STAT3, an essential transcription factor with pleiotropic functions, plays critical roles in the pathogenesis of autoimmunity. Despite recent data linking STAT3 with inflammatory bowel disease, exactly how it contributes to chronic intestinal inflammation is not known. Using a T cell transfer model of colitis we found that STAT3 expression in T cells was essential for the induction of both colitis and systemic inflammation. STAT3 was critical in modulating the balance of T helper 17 (Th17) and regulatory T (Treg) cells, as well as in promoting CD4+ T cell proliferation. We used chromatin immunoprecipitation and massive parallel sequencing (ChIP-Seq) to define the genome-wide targets of STAT3 in CD4+ T cells. We found that STAT3 bound to multiple genes involved in Th17 cell differentiation, cell activation, proliferation and survival, regulating both expression and epigenetic modifications. Thus, STAT3 orchestrates multiple critical aspects of T cell function in inflammation and homeostasis.


systematic_name: M7442
exact_source: GSE21670_2385_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with TGF beta: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7443
exact_source: GSE21670_2385_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with TGF beta: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7444
exact_source: GSE21670_2386_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7446
exact_source: GSE21670_2374_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: TGF beta versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7447
exact_source: GSE21670_2374_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: TGF beta versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7448
exact_source: GSE21670_2375_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: TGF beta versus IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7449
exact_source: GSE21670_2376_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: IL6 [GeneID=3569] versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7451
exact_source: GSE21670_2376_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: IL6 [GeneID=3569] versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7452
exact_source: GSE21670_2389_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with TGF beta and IL6 [GeneID=3569]: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7453
exact_source: GSE21670_2389_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with TGF beta and IL6 [GeneID=3569]: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7457
exact_source: GSE21670_2383_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7458
exact_source: GSE21670_2383_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7463
exact_source: GSE21670_2380_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus TGF beta.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7464
exact_source: GSE21670_2379_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: IL6 [GeneID=3569] versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7469
exact_source: GSE21670_2388_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with IL6 [GeneID=3569]: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7473
exact_source: GSE21670_2379_200_DN
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: IL6 [GeneID=3569] versus TGF beta and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7474
exact_source: GSE21670_2380_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells with STAT3 [GeneID=6774] knockout: medium versus TGF beta.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7475
exact_source: GSE21670_2388_200_UP
source_species_code: MM
GEO_id: GSE21670
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with IL6 [GeneID=3569]: STAT3 [GeneID=6774] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1005 characters]


systematic_name: M7478
exact_source: GSE22229_2395_200_UP
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in periperal blood monocytes (PBMC) from kidney transplant recipients: tolerant versus immunosuppressive therapy.

description_full:
  In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable allograft function while on immunosuppression and healthy non transplated, controls. Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression. Microarrays were used to detect expressed gene profiles of whole-blood total RNA from subjects in the tolerant, standard immunotherapy and healthy control participants


systematic_name: M7479
exact_source: GSE22229_2397_200_DN
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in periperal blood monocytes (PBMC): kidney transplant recipients receiving immunosuppression therapy versus healthy controls.

description_full:
  In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable allograft function while on immunosuppression and healthy non transplated, controls. Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression. Microarrays were used to detect expressed gene profiles of whole-blood total RNA from subjects in the tolerant, standard immunotherapy and healthy control participants


systematic_name: M7480
exact_source: GSE22229_2396_200_DN
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in periperal blood monocytes (PBMC): tolerant kidney transplants versus healthy controls.

description_full:
  In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable allograft function while on immunosuppression and healthy non transplated, controls. Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression. Microarrays were used to detect expressed gene profiles of whole-blood total RNA from subjects in the tolerant, standard immunotherapy and healthy control participants


systematic_name: M7483
exact_source: GSE22229_2397_200_UP
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in periperal blood monocytes (PBMC): kidney transplant recipients receiving immunosuppression therapy versus healthy controls.

description_full:
[cell repeats an earlier one in this file: 691 characters]


systematic_name: M7485
exact_source: GSE22229_2395_200_DN
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in periperal blood monocytes (PBMC) from kidney transplant recipients: tolerant versus immunosuppressive therapy.

description_full:
[cell repeats an earlier one in this file: 691 characters]


systematic_name: M7486
exact_source: GSE22229_2396_200_UP
source_species_code: HS
GEO_id: GSE22229
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in periperal blood monocytes (PBMC): tolerant kidney transplants versus healthy controls.

description_full:
[cell repeats an earlier one in this file: 691 characters]


systematic_name: M7489
exact_source: GSE21774_3813_200_UP
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in NCAM+ [GeneID=4684] NK cells: SELL bright [GeneID=6402] versus SELL dim [GeneID=6402].

description_full:
  Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors.


systematic_name: M7490
exact_source: GSE21774_3814_200_UP
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in NCAM1+ SELL bright [GeneID=4684;6402] versus NCAM1- SELL dim [GeneID=4684;6402].

description_full:
  Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors.


systematic_name: M7491
exact_source: GSE21774_3815_200_UP
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in SELL dim [GeneID=6402] NK cells: NCAM1+ [GeneID=4684] versus NCAM1- [GeneID=4684].

description_full:
  Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors.


systematic_name: M7492
exact_source: GSE21774_3813_200_DN
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in NCAM+ [GeneID=4684] NK cells: SELL bright [GeneID=6402] versus SELL dim [GeneID=6402].

description_full:
[cell repeats an earlier one in this file: 1282 characters]


systematic_name: M7495
exact_source: GSE21774_3814_200_DN
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in NCAM1+ SELL bright [GeneID=4684;6402] versus NCAM1- SELL dim [GeneID=4684;6402].

description_full:
[cell repeats an earlier one in this file: 1282 characters]


systematic_name: M7496
exact_source: GSE21774_3815_200_DN
source_species_code: HS
GEO_id: GSE21774
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in SELL dim [GeneID=6402] NK cells: NCAM1+ [GeneID=4684] versus NCAM1- [GeneID=4684].

description_full:
[cell repeats an earlier one in this file: 1282 characters]


systematic_name: M7498
exact_source: GSE21379_3025_200_DN
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] follicular helper T cells (Tfh) with SH2D1A [GeneID=4068] knockout versus wildtype Tfh cells.

description_full:
  CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation.


systematic_name: M7499
exact_source: GSE21379_3026_200_UP
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] non-follicular helper T cells: wildtype versus SH2D1A [GeneID=4068] knockout.

description_full:
  CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation.


systematic_name: M7501
exact_source: GSE21379_3025_200_UP
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] follicular helper T cells (Tfh) with SH2D1A [GeneID=4068] knockout versus wildtype Tfh cells.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7503
exact_source: GSE21380_2731_200_UP
source_species_code: MM
GEO_id: GSE21380
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: non-Tfh versus Tfh (T follicular helper) from germinal center.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7505
exact_source: GSE21380_2731_200_DN
source_species_code: MM
GEO_id: GSE21380
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: non-Tfh versus Tfh (T follicular helper) from germinal center.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7506
exact_source: GSE21380_2732_200_UP
source_species_code: MM
GEO_id: GSE21380
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] Tfh (T follicular helper) cells: Tfh versus Tfh from germinal center.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7509
exact_source: GSE21380_2732_200_DN
source_species_code: MM
GEO_id: GSE21380
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] Tfh (T follicular helper) cells: Tfh versus Tfh from germinal center.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7510
exact_source: GSE21379_3024_200_DN
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] follicular helper T cells (Tfh) with SH2D1A [GeneID=4068] knockout versus non-Tfh cells with SH2D1A [GeneID=4068] knockout.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7511
exact_source: GSE21379_3026_200_DN
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] non-follicular helper T cells: wildtype versus SH2D1A [GeneID=4068] knockout.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7516
exact_source: GSE21379_3024_200_UP
source_species_code: MM
GEO_id: GSE21379
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] follicular helper T cells (Tfh) with SH2D1A [GeneID=4068] knockout versus non-Tfh cells with SH2D1A [GeneID=4068] knockout.

description_full:
[cell repeats an earlier one in this file: 1485 characters]


systematic_name: M7518
exact_source: GSE21546_3639_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated double positive thymocytes: wildtype versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
  Removal of the transcription factor SAP1a member of the Ternary Complex Factor (TCF) group of transcription factors which in conjunction with Serum Response Factor (SRF) has been shown to have a profound effect on positive selection in the thymus. When another TCF Elk1 is knocked out in mice there is no effect on positive selection unless it is on a Sap1a KO background where the phenotype is very severe. We have stimulated isolated double positive T cells (DPs) with anti-CD3 to mimic positive selection and compared basal and stimulated transcription across the four genotypes to discover the downstream targets of Sap1a involved in positive selection.


systematic_name: M7519
exact_source: GSE21546_3640_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK4 [GeneID=2005] knockout.

description_full:
  Removal of the transcription factor SAP1a member of the Ternary Complex Factor (TCF) group of transcription factors which in conjunction with Serum Response Factor (SRF) has been shown to have a profound effect on positive selection in the thymus. When another TCF Elk1 is knocked out in mice there is no effect on positive selection unless it is on a Sap1a KO background where the phenotype is very severe. We have stimulated isolated double positive T cells (DPs) with anti-CD3 to mimic positive selection and compared basal and stimulated transcription across the four genotypes to discover the downstream targets of Sap1a involved in positive selection.


systematic_name: M7520
exact_source: GSE21546_3638_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated double positive thymocytes: wildtype versus ELK1 [GeneID=2002] knockout.

description_full:
  Removal of the transcription factor SAP1a member of the Ternary Complex Factor (TCF) group of transcription factors which in conjunction with Serum Response Factor (SRF) has been shown to have a profound effect on positive selection in the thymus. When another TCF Elk1 is knocked out in mice there is no effect on positive selection unless it is on a Sap1a KO background where the phenotype is very severe. We have stimulated isolated double positive T cells (DPs) with anti-CD3 to mimic positive selection and compared basal and stimulated transcription across the four genotypes to discover the downstream targets of Sap1a involved in positive selection.


systematic_name: M7522
exact_source: GSE21546_3642_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7523
exact_source: GSE21546_3643_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated double positive thymocytes: ELK4 [GeneID=2005] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7524
exact_source: GSE21546_3643_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated double positive thymocytes: ELK4 [GeneID=2005] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7525
exact_source: GSE21546_3644_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes stimulated by anti-CD3: ELK4 [GeneID=2005] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7526
exact_source: GSE21546_3644_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes stimulated by anti-CD3: ELK4 [GeneID=2005] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7527
exact_source: GSE21546_3638_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated double positive thymocytes: wildtype versus ELK1 [GeneID=2002] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7529
exact_source: GSE21546_3639_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated double positive thymocytes: wildtype versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7530
exact_source: GSE21546_3646_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in stimulated by anti-CD3 double positive thymocytes: ELK1 [GeneID=2002] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7531
exact_source: GSE21546_3646_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in stimulated by anti-CD3 double positive thymocytes: ELK1 [GeneID=2002] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7532
exact_source: GSE21546_3640_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK4 [GeneID=2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7535
exact_source: GSE21546_3641_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK1 [GeneID=2002] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7536
exact_source: GSE21546_3634_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes with ELK4 [GeneID=2005] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7537
exact_source: GSE21546_3635_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes with ELK1 [GeneID=2002] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7538
exact_source: GSE21546_3635_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes with ELK1 [GeneID=2002] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7539
exact_source: GSE21546_3636_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes with ELK1 and ELK4 [GeneID=2002;2005] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7541
exact_source: GSE21546_3636_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes with ELK1 and ELK4 [GeneID=2002;2005] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7543
exact_source: GSE21546_3637_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated double positive thymocytes: wildtype versus ELK4 [GeneID=2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7544
exact_source: GSE21546_3637_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated double positive thymocytes: wildtype versus ELK4 [GeneID=2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7545
exact_source: GSE21546_3645_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated double positive thymocytes: ELK1 [GeneID=2002] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7546
exact_source: GSE21546_3645_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated double positive thymocytes: ELK1 [GeneID=2002] knockout versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7550
exact_source: GSE21546_3634_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes with ELK4 [GeneID=2005] knockout: untreated versus stimulated by anti-CD3.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7551
exact_source: GSE21546_3641_200_DN
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK1 [GeneID=2002] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7553
exact_source: GSE21546_3642_200_UP
source_species_code: MM
GEO_id: GSE21546
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double positive thymocytes stimulated by anti-CD3: wildtype versus ELK1 and ELK4 [GeneID=2002;2005] knockout.

description_full:
[cell repeats an earlier one in this file: 657 characters]


systematic_name: M7554
exact_source: GSE21927_2528_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b BoneMarrow from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and IL-6.

description_full:
  Tumor growth is associated with a profound alteration of myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). Analyzing the cytokines affecting myelo-monocytic differentiation produced by various experimental tumors, we found that GM-CSF, G-CSF, and IL-6 allowed a rapid generation of MDSCs from precursors present in mouse and human bone marrow (BM). BM-MDSCs induced by GM-CSF+IL-6 possessed the highest tolerogenic activity, as revealed by the ability to impair the priming of IFN- -producing CD8+ T cells upon in vivo adoptive transfer. Moreover, adoptive transfer of syngeneic, GM-CSF+IL-6-conditioned MDSCs to diabetic mice transplanted with allogeneic pancreatic islets resulted in long term acceptance of the allograft and correction of the diabetic status. Cytokines inducing MDSCs acted on a common molecular pathway. Immunoregulatory activity of both tumor-induced and BM-derived MDSCs was entirely dependent on C/EBP transcription factor, a key component of the emergency myelopoiesis triggered by stress and inflammation. Adoptive transfer of tumor antigen-specific CD8+ T lymphocytes resulted in therapy of established tumors only in mice lacking C/EBP in myeloid compartment. These data unveil another link between inflammation and cancer and identify a novel molecular target to control tumor-induced immune suppression. We used gene expression analysis to identify those factors, secreted by tumor-infiltrating MDSC, which could drive emathopoiesis. Moreover we compare gene expression profile of tumor-induced MDSC, obtained from either the spleen and the tumor infiltrate of tumor bearing mice, and in vitro bone marrow-derived MDSC.


systematic_name: M7555
exact_source: GSE21927_2516_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from spleen of BALB/c mice: healthy versus bearing C26GM colon carcinoma.

description_full:
  Tumor growth is associated with a profound alteration of myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). Analyzing the cytokines affecting myelo-monocytic differentiation produced by various experimental tumors, we found that GM-CSF, G-CSF, and IL-6 allowed a rapid generation of MDSCs from precursors present in mouse and human bone marrow (BM). BM-MDSCs induced by GM-CSF+IL-6 possessed the highest tolerogenic activity, as revealed by the ability to impair the priming of IFN- -producing CD8+ T cells upon in vivo adoptive transfer. Moreover, adoptive transfer of syngeneic, GM-CSF+IL-6-conditioned MDSCs to diabetic mice transplanted with allogeneic pancreatic islets resulted in long term acceptance of the allograft and correction of the diabetic status. Cytokines inducing MDSCs acted on a common molecular pathway. Immunoregulatory activity of both tumor-induced and BM-derived MDSCs was entirely dependent on C/EBP transcription factor, a key component of the emergency myelopoiesis triggered by stress and inflammation. Adoptive transfer of tumor antigen-specific CD8+ T lymphocytes resulted in therapy of established tumors only in mice lacking C/EBP in myeloid compartment. These data unveil another link between inflammation and cancer and identify a novel molecular target to control tumor-induced immune suppression. We used gene expression analysis to identify those factors, secreted by tumor-infiltrating MDSC, which could drive emathopoiesis. Moreover we compare gene expression profile of tumor-induced MDSC, obtained from either the spleen and the tumor infiltrate of tumor bearing mice, and in vitro bone marrow-derived MDSC.


systematic_name: M7556
exact_source: GSE21927_2517_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from BALB/c mice bearing C26GM colon carcinoma: spleen of BALB/c mice: spleen versus tumor infiltrating monocytes.

description_full:
  Tumor growth is associated with a profound alteration of myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). Analyzing the cytokines affecting myelo-monocytic differentiation produced by various experimental tumors, we found that GM-CSF, G-CSF, and IL-6 allowed a rapid generation of MDSCs from precursors present in mouse and human bone marrow (BM). BM-MDSCs induced by GM-CSF+IL-6 possessed the highest tolerogenic activity, as revealed by the ability to impair the priming of IFN- -producing CD8+ T cells upon in vivo adoptive transfer. Moreover, adoptive transfer of syngeneic, GM-CSF+IL-6-conditioned MDSCs to diabetic mice transplanted with allogeneic pancreatic islets resulted in long term acceptance of the allograft and correction of the diabetic status. Cytokines inducing MDSCs acted on a common molecular pathway. Immunoregulatory activity of both tumor-induced and BM-derived MDSCs was entirely dependent on C/EBP transcription factor, a key component of the emergency myelopoiesis triggered by stress and inflammation. Adoptive transfer of tumor antigen-specific CD8+ T lymphocytes resulted in therapy of established tumors only in mice lacking C/EBP in myeloid compartment. These data unveil another link between inflammation and cancer and identify a novel molecular target to control tumor-induced immune suppression. We used gene expression analysis to identify those factors, secreted by tumor-infiltrating MDSC, which could drive emathopoiesis. Moreover we compare gene expression profile of tumor-induced MDSC, obtained from either the spleen and the tumor infiltrate of tumor bearing mice, and in vitro bone marrow-derived MDSC.


systematic_name: M7558
exact_source: GSE21927_2516_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from spleen of BALB/c mice: healthy versus bearing C26GM colon carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7560
exact_source: GSE21927_2518_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from BALB/c mice bearing 4T1 mammary carcinoma: spleen of BALB/c mice: spleen versus tumor infiltrating monocytes.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7563
exact_source: GSE21927_2520_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from BALB/c mice bearing: C26GM colon carcinoma versus 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7564
exact_source: GSE21927_2526_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b Spleen from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7565
exact_source: GSE21927_2526_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b Spleen from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7567
exact_source: GSE21927_2528_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b BoneMarrow from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and IL-6.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7571
exact_source: GSE21927_2529_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b BoneMarrow from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7572
exact_source: GSE21927_2530_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b BoneMarrow from BALBc mouse incubated with GMCSF and IL-6 versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7573
exact_source: GSE21927_2517_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from BALB/c mice bearing C26GM colon carcinoma: spleen of BALB/c mice: spleen versus tumor infiltrating monocytes.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7574
exact_source: GSE21927_2518_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from BALB/c mice bearing 4T1 mammary carcinoma: spleen of BALB/c mice: spleen versus tumor infiltrating monocytes.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7584
exact_source: GSE21927_2527_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b EL4 Tumor from C57BL6 mouse versus CD11b MCA203 Tumor from C57BL6 mouse.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7586
exact_source: GSE21927_2527_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b EL4 Tumor from C57BL6 mouse versus CD11b MCA203 Tumor from C57BL6 mouse.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7587
exact_source: GSE21927_2521_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from BALB/c mice bearing C26GM colon carcinoma: spleen versus tumor.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7588
exact_source: GSE21927_2529_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b BoneMarrow from BALBc mouse versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7589
exact_source: GSE21927_2522_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from spleen of BALB/c mice bearing C26GM colon carcinoma versus CD11b+ cells from tumors of BALB/c mice bearing 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7590
exact_source: GSE21927_2522_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from spleen of BALB/c mice bearing C26GM colon carcinoma versus CD11b+ cells from tumors of BALB/c mice bearing 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7592
exact_source: GSE21927_2523_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from spleen of BALB/c mice bearing C26GM colon carcinoma versus CD11b+ cells from bone marrow of healthy BALB/c mice.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7593
exact_source: GSE21927_2523_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from spleen of BALB/c mice bearing C26GM colon carcinoma versus CD11b+ cells from bone marrow of healthy BALB/c mice.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7594
exact_source: GSE21927_2524_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ cells from spleen of healthy C57BL6 mice versus CD11b+ cells from tumor infiltrating monocytes of BALB/c mice bearing 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7595
exact_source: GSE21927_2524_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from spleen of healthy C57BL6 mice versus CD11b+ cells from tumor infiltrating monocytes of BALB/c mice bearing 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7596
exact_source: GSE21927_2525_200_UP
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD11b+ from spleen of healthy C57BL6 versus CD11b+ cells from tumors of C57BL6 mice bearing EL4 lymphoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7599
exact_source: GSE21927_2525_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ from spleen of healthy C57BL6 versus CD11b+ cells from tumors of C57BL6 mice bearing EL4 lymphoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7605
exact_source: GSE21927_2521_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from BALB/c mice bearing C26GM colon carcinoma: spleen versus tumor.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7607
exact_source: GSE21927_2520_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b+ cells from BALB/c mice bearing: C26GM colon carcinoma versus 4T1 mammary carcinoma.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


systematic_name: M7609
exact_source: GSE21927_2530_200_DN
source_species_code: MM
GEO_id: GSE21927
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD11b BoneMarrow from BALBc mouse incubated with GMCSF and IL-6 versus CD11b BoneMarrow from BALBc mouse incubated with GMCSF and GCSF.

description_full:
[cell repeats an earlier one in this file: 1714 characters]


description_brief: Genes down-regulated in memory CD8 T cells: 1' versus 4'.
systematic_name: M7610
exact_source: GSE21360_1269_200_DN
source_species_code: MM
GEO_id: GSE21360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The transcriptome of naive OT-I T cells was compared to memory CD8 T cells after 1, 2, 3, or 4 infection with ovalbumin expressing Listeria monocytogenes (LM-OVA).


description_brief: Genes down-regulated in healthy CD4 [GeneID=920] T cells: germ free versus specific pathogen free.
systematic_name: M7644
exact_source: GSE22140_2813_200_DN
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  A general defect of GF K/BxN T cell proliferation response toward antigen motivated us to look for the impairment in GF K/BxN T cells that might leads to the low Ab production and reduced disease phenotype seen in GF K/BxN mice. To find the difference between GF and SPF K/BxN T cells in a broad and non-biased fashion, we performed gene-expression profiling of these cells using microarrays.


systematic_name: M7645
exact_source: GSE22140_2815_200_DN
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in arthritic (KRN model) CD4 [GeneID=920] T cells: germ free versus specific pathogen free conditions.

description_full:
  A general defect of GF K/BxN T cell proliferation response toward antigen motivated us to look for the impairment in GF K/BxN T cells that might leads to the low Ab production and reduced disease phenotype seen in GF K/BxN mice. To find the difference between GF and SPF K/BxN T cells in a broad and non-biased fashion, we performed gene-expression profiling of these cells using microarrays.


systematic_name: M7646
exact_source: GSE22140_2812_200_DN
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells under germ free conditions: healthy versus arthritis (KRN model).

description_full:
  A general defect of GF K/BxN T cell proliferation response toward antigen motivated us to look for the impairment in GF K/BxN T cells that might leads to the low Ab production and reduced disease phenotype seen in GF K/BxN mice. To find the difference between GF and SPF K/BxN T cells in a broad and non-biased fashion, we performed gene-expression profiling of these cells using microarrays.


systematic_name: M7648
exact_source: GSE22140_2812_200_UP
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells under germ free conditions: healthy versus arthritis (KRN model).

description_full:
[cell repeats an earlier one in this file: 392 characters]


systematic_name: M7649
exact_source: GSE22140_2815_200_UP
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in arthritic (KRN model) CD4 [GeneID=920] T cells: germ free versus specific pathogen free conditions.

description_full:
[cell repeats an earlier one in this file: 392 characters]


systematic_name: M7650
exact_source: GSE22140_2814_200_UP
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells under specific pathogen free conditions: healthy versus arthritis (KRN model).

description_full:
[cell repeats an earlier one in this file: 392 characters]


systematic_name: M7651
exact_source: GSE22140_2814_200_DN
source_species_code: MM
GEO_id: GSE22140
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells under specific pathogen free conditions: healthy versus arthritis (KRN model).

description_full:
[cell repeats an earlier one in this file: 392 characters]


description_brief: Genes down-regulated in skin gamma delta T cells: healthy versus obesity.
systematic_name: M7653
exact_source: GSE22196_3829_200_DN
source_species_code: MM
GEO_id: GSE22196
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Epithelial cells provide an initial line of defense against damage and pathogens in barrier tissues such as the skin; however this balance is disrupted in obesity and metabolic disease. Skin gamma delta T cells recognize epithelial damage and release cytokines and growth factors that facilitate wound repair. To determine the impact of obesity and metabolic disease on skin gamma delta T cells, we isolated skin gamma delta T cells from 10-week old C57BLKS/J lean db/+ and obese db/db animals for further study. Due to a deficiency in the leptin receptor (db), homozygous db/db animals do not process satiety signals, continually eat and develop severe obesity and metabolic disease. Skin gamma delta T cells isolated from these animals were compared for changes in mRNA expression using microarray. We have determined that obesity and metabolic disease negatively impacts homeostasis and functionality of skin gamma delta T cells, rendering host defense mechanisms vulnerable to injury and infection.


systematic_name: M7656
exact_source: GSE19401_2536_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ex vivo follicular dendritic cells from peripheral lymph nodes: naïve versus immunized mice.

description_full:
  Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyer’s patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown. To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs.


systematic_name: M7658
exact_source: GSE19401_2536_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ex vivo follicular dendritic cells from peripheral lymph nodes: naïve versus immunized mice.

description_full:
  Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyer’s patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown. To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs.


systematic_name: M7659
exact_source: GSE19401_2539_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: non-stimulated versus tretinoin [PubChem=444795] and Pam2CSK4 (96h).

description_full:
  Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyer’s patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown. To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs.


systematic_name: M7661
exact_source: GSE19401_2538_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: non-stimulated versus tretinoin [PubChem=444795] (96h).

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7664
exact_source: GSE19401_2538_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: non-stimulated versus tretinoin [PubChem=444795] (96h).

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7665
exact_source: GSE19401_2539_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: non-stimulated versus tretinoin [PubChem=444795] and Pam2CSK4 (96h).

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7666
exact_source: GSE19401_2535_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ex vivo follicular dendritic cells: peripheral lymph node versus Peyers patch.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7667
exact_source: GSE19401_2535_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ex vivo follicular dendritic cells: peripheral lymph node versus Peyers patch.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7668
exact_source: GSE19401_2541_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): Pam2CSK4 versus tretinoin [PubChem=444795] and Pam2CSK4.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7670
exact_source: GSE19401_2537_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: unstimulated versus Pam2CSK4 (96h).

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7671
exact_source: GSE19401_2537_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes: unstimulated versus Pam2CSK4 (96h).

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7672
exact_source: GSE19401_2540_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): Pam2CSK4 versus tretinoin [PubChem=444795].

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7673
exact_source: GSE19401_2541_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): Pam2CSK4 versus tretinoin [PubChem=444795] and Pam2CSK4.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7674
exact_source: GSE19401_2540_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): Pam2CSK4 versus tretinoin [PubChem=444795].

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7679
exact_source: GSE19401_2542_200_DN
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): tretinoin [PubChem=444795] versus tretinoin [PubChem=444795] and Pam2CSK4.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7680
exact_source: GSE19401_2542_200_UP
source_species_code: MM
GEO_id: GSE19401
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in the in vitro follicular dendritic cells from peripheral lymph nodes (96h): tretinoin [PubChem=444795] versus tretinoin [PubChem=444795] and Pam2CSK4.

description_full:
[cell repeats an earlier one in this file: 686 characters]


systematic_name: M7681
exact_source: GSE20152_3103_200_DN
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ankle joints from SPHK1 [GeneID=8877] knockout: TNF [GeneID=7124] over-expression versus control.

description_full:
  The study analyzes analyzes gene expression changes in the ankle joint in mouse TNFa overexpression models with or without sphingosine kinase 1 activity. SphK1 is a sphingolipid enzyme that converts sphingosine to bioactive sphingosine-1-phosphate (S1P). Recent data suggest a potential relationship between SphK1 and TNFα and have implicated SphK1/S1P in the development and progression of inflammation. Here we further study the relationship of TNFα and SphK1 using an in vivo model. Transgenic hTNFα mice, which develop a spontaneous arthritis (limited to paws) at 20 weeks, were crossed with SphK1 activity null mice (SphK1-/-) to study the development of inflammatory arthritis in the functional absence of SphK1. Results show that hTNF/SphK1-/- have significantly less severity and progression of arthritis and bone erosions as measured through micro-CT images. Additionally, less COX-2 protein, mTNFα transcript levels and fewer Th 17 cells were detected in the joints of hTNF/SphK1-/- compared to hTNF/SphK1+/+ mice. Microarray analysis of the ankle joint showed that hTNF/SphK1-/- mice have increased transcript levels of IL-6 and SOCS3 compared to hTNF/SphK1+/+ mice. Finally, fewer mature osteoclasts were detected in the ankle joints of hTNF/SphK1-/- mice compared to hTNF/SphK1+/+ mice. These data show that SphK1 plays a role in hTNFα induced inflammatory arthritis, potentially through a novel pathway involving IL-6 and SOCS3.


systematic_name: M7682
exact_source: GSE20152_3105_200_UP
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ankle joints: SPHK1 [GeneID=8877] versus wildtype over-expressing TNF [GeneID=7124].

description_full:
  The study analyzes analyzes gene expression changes in the ankle joint in mouse TNFa overexpression models with or without sphingosine kinase 1 activity. SphK1 is a sphingolipid enzyme that converts sphingosine to bioactive sphingosine-1-phosphate (S1P). Recent data suggest a potential relationship between SphK1 and TNFα and have implicated SphK1/S1P in the development and progression of inflammation. Here we further study the relationship of TNFα and SphK1 using an in vivo model. Transgenic hTNFα mice, which develop a spontaneous arthritis (limited to paws) at 20 weeks, were crossed with SphK1 activity null mice (SphK1-/-) to study the development of inflammatory arthritis in the functional absence of SphK1. Results show that hTNF/SphK1-/- have significantly less severity and progression of arthritis and bone erosions as measured through micro-CT images. Additionally, less COX-2 protein, mTNFα transcript levels and fewer Th 17 cells were detected in the joints of hTNF/SphK1-/- compared to hTNF/SphK1+/+ mice. Microarray analysis of the ankle joint showed that hTNF/SphK1-/- mice have increased transcript levels of IL-6 and SOCS3 compared to hTNF/SphK1+/+ mice. Finally, fewer mature osteoclasts were detected in the ankle joints of hTNF/SphK1-/- mice compared to hTNF/SphK1+/+ mice. These data show that SphK1 plays a role in hTNFα induced inflammatory arthritis, potentially through a novel pathway involving IL-6 and SOCS3.


systematic_name: M7683
exact_source: GSE20152_3105_200_DN
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ankle joints: SPHK1 [GeneID=8877] versus wildtype over-expressing TNF [GeneID=7124].

description_full:
  The study analyzes analyzes gene expression changes in the ankle joint in mouse TNFa overexpression models with or without sphingosine kinase 1 activity. SphK1 is a sphingolipid enzyme that converts sphingosine to bioactive sphingosine-1-phosphate (S1P). Recent data suggest a potential relationship between SphK1 and TNFα and have implicated SphK1/S1P in the development and progression of inflammation. Here we further study the relationship of TNFα and SphK1 using an in vivo model. Transgenic hTNFα mice, which develop a spontaneous arthritis (limited to paws) at 20 weeks, were crossed with SphK1 activity null mice (SphK1-/-) to study the development of inflammatory arthritis in the functional absence of SphK1. Results show that hTNF/SphK1-/- have significantly less severity and progression of arthritis and bone erosions as measured through micro-CT images. Additionally, less COX-2 protein, mTNFα transcript levels and fewer Th 17 cells were detected in the joints of hTNF/SphK1-/- compared to hTNF/SphK1+/+ mice. Microarray analysis of the ankle joint showed that hTNF/SphK1-/- mice have increased transcript levels of IL-6 and SOCS3 compared to hTNF/SphK1+/+ mice. Finally, fewer mature osteoclasts were detected in the ankle joints of hTNF/SphK1-/- mice compared to hTNF/SphK1+/+ mice. These data show that SphK1 plays a role in hTNFα induced inflammatory arthritis, potentially through a novel pathway involving IL-6 and SOCS3.


systematic_name: M7684
exact_source: GSE20152_3104_200_UP
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ankle joints over-expressing TNF [GeneID=7124]: SPHK1 [GeneID=8877] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1442 characters]


systematic_name: M7686
exact_source: GSE20152_3104_200_DN
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ankle joints over-expressing TNF [GeneID=7124]: SPHK1 [GeneID=8877] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1442 characters]


systematic_name: M7687
exact_source: GSE20152_3103_200_UP
source_species_code: MM
GEO_id: GSE20152
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ankle joints from SPHK1 [GeneID=8877] knockout: TNF [GeneID=7124] over-expression versus control.

description_full:
[cell repeats an earlier one in this file: 1442 characters]


description_brief: Genes up-regulated in mouse embryonic fibroblasts (MEF): untreated versus MRL24 [PubChem=9958543].
systematic_name: M7688
exact_source: GSE22033_2270_200_UP
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  In order to identify the molecular mechanisms of PPARgamma phosphorylation at Set273, we generated cell-lines of PPARgamma KO MEFs expressing wtPPARgamma or S273APPARgamma. In addition, because our data showed that PPARgamma ligand drugs such as rosiglitazone and MRL24 blocked this phopshorylation, we treated cells with these drugs, then prepared RNA samples to look at the gene profiling.


systematic_name: M7690
exact_source: GSE22033_2269_200_DN
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mouse embryonic fibroblasts (MEF): untreated versus rosiglitazone [PubChem=77999].

description_full:
  In order to identify the molecular mechanisms of PPARgamma phosphorylation at Set273, we generated cell-lines of PPARgamma KO MEFs expressing wtPPARgamma or S273APPARgamma. In addition, because our data showed that PPARgamma ligand drugs such as rosiglitazone and MRL24 blocked this phopshorylation, we treated cells with these drugs, then prepared RNA samples to look at the gene profiling.


systematic_name: M7692
exact_source: GSE22033_2268_200_DN
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mouse embryonic fibroblasts (MEF): wildtype versus PPARG [GeneID=5468] knockout.

description_full:
  In order to identify the molecular mechanisms of PPARgamma phosphorylation at Set273, we generated cell-lines of PPARgamma KO MEFs expressing wtPPARgamma or S273APPARgamma. In addition, because our data showed that PPARgamma ligand drugs such as rosiglitazone and MRL24 blocked this phopshorylation, we treated cells with these drugs, then prepared RNA samples to look at the gene profiling.


systematic_name: M7694
exact_source: GSE22033_2268_200_UP
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mouse embryonic fibroblasts (MEF): wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 391 characters]


systematic_name: M7695
exact_source: GSE22033_2269_200_UP
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mouse embryonic fibroblasts (MEF): untreated versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 391 characters]


systematic_name: M7696
exact_source: GSE22033_2270_200_DN
source_species_code: MM
GEO_id: GSE22033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mouse embryonic fibroblasts (MEF): untreated versus MRL24 [PubChem=9958543].

description_full:
[cell repeats an earlier one in this file: 391 characters]


description_full: This is to determine the T cell genes regulated by retinoic acid.
systematic_name: M7702
exact_source: GSE20500_3217_200_UP
source_species_code: MM
GEO_id: GSE20500
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: tretinoin [PubChem=444795] versus Ro 41-5253 [PubChem=5312120].


description_full: This is to determine the T cell genes regulated by retinoic acid.
systematic_name: M7708
exact_source: GSE20500_3217_200_DN
source_species_code: MM
GEO_id: GSE20500
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: tretinoin [PubChem=444795] versus Ro 41-5253 [PubChem=5312120].


description_brief: Genes down-regulated in T reg following anti-CD3 in vivo treatment versus control.
systematic_name: M7709
exact_source: GSE22527_3555_200_DN
source_species_code: MM
GEO_id: GSE22527
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Treatment with anti-CD3 is a promising therapeutic approach for autoimmune diabetes, but its mechanism of action remains unclear. Foxp3+ regulatory T (Treg) cells may be involved, but the evidence has been conflicting, and there is great uncertainty as to possible mechanistic connections. We investigated this issue in mice derived from the NOD model, which were engineered mice in which Treg populations were perturbed, or could be manipulated by acute ablation or transfer. The data highlighted the involvement of Foxp3+ cells in anti-CD3 action. Rather than a generic influence on all Treg cells, the therapeutic effect seemed to involve an striking expansion of previously constrained Treg cell populations; this expansion occurred not through conversion from Foxp3- Tconv cells but from a dramatic proliferative expansion. We found that Treg cells are normally constrained by TCR-specific niches in secondary lymphoid organs, and that intraclonal competition restrains their possibility for conversion and expansion in the spleen and lymph nodes, much as niche competition limits their selection in the thymus. The strong perturbations induced by anti-CD3 overcame these niche limitations, in a process dependent on receptors for trophic cytokines, interleukin-2 receptor (IL-2R) and IL-7R.


description_brief: Genes down-regulated in bone marrow-derived dendritic cellstreated by poly(IC): 0h versus 3h.
systematic_name: M7711
exact_source: GSE21033_3180_200_DN
source_species_code: MM
GEO_id: GSE21033
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  BACKGROUND: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment. RESULTS: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism. CONCLUSIONS: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.


systematic_name: M7736
exact_source: GSE23308_3376_200_UP
source_species_code: MM
GEO_id: GSE23308
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages treated by corticosterone [PubChem=5839]: wildtype versus NR3C2 [GeneID=4306] knockout.

description_full:
  Inappropriate excess of the steroid hormone aldosterone, which is a mineralocorticoid receptor (MR) agonist, is associated with increased inflammation and risk of cardiovascular disease. MR antagonists are cardioprotective and antiinflammatory in vivo, and evidence suggests that they mediate these effects in part by aldosterone- independent mechanisms. We used affymetrix to characterize the effect of Mineralocorticoid Receptor deletion on macrophage transcriptional profile, and identify its requirement in normal glucocorticoid signalling.


systematic_name: M7744
exact_source: GSE23308_3375_200_DN
source_species_code: MM
GEO_id: GSE23308
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with NR3C2 [GeneID=4306] knockout: untreated versus corticosterone [PubChem=5839].

description_full:
[cell repeats an earlier one in this file: 544 characters]


systematic_name: M7746
exact_source: GSE23308_3375_200_UP
source_species_code: MM
GEO_id: GSE23308
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with NR3C2 [GeneID=4306] knockout: untreated versus corticosterone [PubChem=5839].

description_full:
[cell repeats an earlier one in this file: 544 characters]


systematic_name: M7748
exact_source: GSE23308_3376_200_DN
source_species_code: MM
GEO_id: GSE23308
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages treated by corticosterone [PubChem=5839]: wildtype versus NR3C2 [GeneID=4306] knockout.

description_full:
[cell repeats an earlier one in this file: 544 characters]


systematic_name: M7749
exact_source: GSE22935_2873_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages 24h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
  Nitric oxide (NO) produced by macrophages (MØs) is toxic to both host tissues and invading pathogens and its regulation is therefore essential to suppress host cytotoxicity. MØ arginase 1 (Arg1) inhibits NO production by competing with NO synthases for arginine, the common substrate of NO synthases and arginases. Two signal transduction pathways control Arg1 expression in MØs. First, a MyD88-dependent pathway induces Arg1 in intracellular infections, while a second Stat6-dependent pathway is required for Arg1 expression in alternativelyactivated MØs. We found that mycobacteria-infected MØs produce soluble factors that induce Arg1 in an autocrine-paracrine manner via Stat3. We identify these factors as IL-6, IL-10 and GCSF. We further establish that Arg1 expression is controlled by the MyD88-dependent production of IL-6, IL-10 and G-CSF rather than cell intrinsic MyD88 signaling to Arg1. Our data reveal the MyD88-dependent pathway of Arg1induction following BCG infection requires Stat3 activation and may result in the development of an immunosuppressive niche in granulomas due to the induced Arg1 production in surrounding uninfected MØs


systematic_name: M7751
exact_source: GSE22935_2872_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages 12h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
  Nitric oxide (NO) produced by macrophages (MØs) is toxic to both host tissues and invading pathogens and its regulation is therefore essential to suppress host cytotoxicity. MØ arginase 1 (Arg1) inhibits NO production by competing with NO synthases for arginine, the common substrate of NO synthases and arginases. Two signal transduction pathways control Arg1 expression in MØs. First, a MyD88-dependent pathway induces Arg1 in intracellular infections, while a second Stat6-dependent pathway is required for Arg1 expression in alternativelyactivated MØs. We found that mycobacteria-infected MØs produce soluble factors that induce Arg1 in an autocrine-paracrine manner via Stat3. We identify these factors as IL-6, IL-10 and GCSF. We further establish that Arg1 expression is controlled by the MyD88-dependent production of IL-6, IL-10 and G-CSF rather than cell intrinsic MyD88 signaling to Arg1. Our data reveal the MyD88-dependent pathway of Arg1induction following BCG infection requires Stat3 activation and may result in the development of an immunosuppressive niche in granulomas due to the induced Arg1 production in surrounding uninfected MØs


systematic_name: M7753
exact_source: GSE22935_2873_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages 24h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7756
exact_source: GSE22935_2882_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with MYD88 [GeneID=4615] knockout after M. bovis BCG infection: 24h versus 48h.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7758
exact_source: GSE22935_2878_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 12h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7764
exact_source: GSE22935_2872_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages 12h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7765
exact_source: GSE22935_2880_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 48h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7766
exact_source: GSE22935_2874_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages 48h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7767
exact_source: GSE22935_2874_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages 48h after M. bovis BCG infection: wildtype versus MYD88 [GeneID=4615] knockout.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7771
exact_source: GSE22935_2879_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 24h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7773
exact_source: GSE22935_2882_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with MYD88 [GeneID=4615] knockout after M. bovis BCG infection: 24h versus 48h.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7774
exact_source: GSE22935_2880_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 48h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7780
exact_source: GSE22935_2878_200_DN
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 12h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


systematic_name: M7781
exact_source: GSE22935_2879_200_UP
source_species_code: MM
GEO_id: GSE22935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated macrophages with MYD88 [GeneID=4615] knockout: untreated versus 24h after M. bovis BCG infection.

description_full:
[cell repeats an earlier one in this file: 1153 characters]


description_brief: Genes down-regulated in memory CD8 T cells: wildtype versus TCF7 [GeneID=6932] knockout.
systematic_name: M7782
exact_source: GSE20754_2450_200_DN
source_species_code: MM
GEO_id: GSE20754
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  TCF-1 is an HMG family transcription factor which is known to be activated by the canonical Wnt signaling pathway and modulated by other signals such as those derived from T cell receptor. We found that during CD8 T cell responses, TCF-1 deficiency impaired long-term maintenance of antigen-specific memory CD8 T cells. We used microarrays to detect gene expression changes in memory CD8 T cells caused by TCF-1 deficiency.


description_brief: Genes up-regulated in NK cells: B3GAT1+ [GeneID=27087] versus B3GAT1- [GeneID=27087].
systematic_name: M7784
exact_source: GSE23695_3368_200_UP
source_species_code: HS
GEO_id: GSE23695
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Thirty to 60% of CD56dimCD16bright NK cells in healthy adults express CD57, which is not expressed on immature CD56bright NK cells or fetal and newborn NK cells. We hypothesized that CD57+ NK cells within the CD56dim mature NK cell subset are highly mature and might be terminally differentiated. We used microarrays to assess the transcriptional differences between CD57+ and CD57neg NK cells within the CD56dim mature NK subset.


description_brief: Genes up-regulated in neutrophils: untreated versus stimulated by CSF2 and IFNG [GeneID=1437;3458].
systematic_name: M7789
exact_source: GSE22103_3648_200_UP
source_species_code: HS
GEO_id: GSE22103
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Neutrophils play critical roles in modulating the immune response. However, neutrophils have a short circulating half life, are readily stimulated in vitro, and have low levels of cellular mRNA when compared to other blood leukocyte populations. All of these factors have made it difficult to evaluate neutrophils from clinical populations for molecular and functional studies. Here we present a robust methodology for rapidly isolating neutrophils directly from whole blood and develop ‘on- chip’ processing for mRNA and protein isolation for genomics and proteomics. We validate this device with an ex vivo stimulation experiment and demonstrate the ability of the device to discriminate subtle differences in the genomic and proteomic response of peripheral blood neutrophils to direct and indirect stimulation. Lastly, we implement this tool as part of a near patient blood processing system within a multi-center clinical study of the immune response to severe trauma and burn injury and demonstrate that this technique is easy to use by nurses and technical staff yielding excellent quality and sufficient quantity of mRNA for sensitive genomic readout of the host response to injury


systematic_name: M7792
exact_source: GSE22103_3648_200_DN
source_species_code: HS
GEO_id: GSE22103
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in neutrophils: untreated versus stimulated by CSF2 and IFNG [GeneID=1437;3458].

description_full:
[cell repeats an earlier one in this file: 1189 characters]


description_brief: Genes down-regulated in monocyte-derived dendritic cells: control versus HIV and SIV infection.
systematic_name: M7796
exact_source: GSE22589_3652_200_DN
source_species_code: HS
GEO_id: GSE22589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Dendritic cells (DC) serve a key function in host defense, linking innate detection of microbes to the activation of pathogen-specific adaptive immune responses. Whether there is cell-intrinsic recognition of HIV-1 by host innate pattern-recognition receptors and subsequent coupling to antiviral T cell responses is not yet known. DC are largely resistant to infection with HIV-1, but facilitate infection of co-cultured T-helper cells through a process of trans-enhancement. We show here that, when DC resistance to infection is circumvented, HIV-1 induces DC maturation, an antiviral type I interferon response and activation of T cells. This innate response is dependent on the interaction of newly-synthesized HIV-1 capsid (CA) with cellular cyclophilin A (CypA) and the subsequent activation of the transcription factor IRF3. Because the peptidyl-prolyl isomerase CypA also interacts with CA to promote HIV-1 infectivity, our results suggest that CA conformation has evolved under opposing selective pressures for infectivity versus furtiveness. Thus, a cell intrinsic sensor for HIV-1 exists in DC and mediates an antiviral immune response, but it is not typically engaged due to absence of DC infection. The virulence of HIV-1 may be related to evasion of this response, whose manipulation may be necessary to generate an effective HIV-1 vaccine.


description_brief: Genes up-regulated in dendritic cells: common versus plasmacytoid.
systematic_name: M7811
exact_source: GSE22432_3612_200_UP
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Dendritic cells (DCs) in lymphoid tissue comprise conventional DCs (cDCs) and plasmacytoid DCs (pDCs) that develop from common DC progenitors (CDPs). CDPs are Flt3+c-kitintM-CSFR+ and reside in bone marrow. Here we describe a two-step culture system that recapitulates DC development from c-kithiFlt3-/lo multipotent progenitors (MPPs) into CDPs and further into cDC and pDC subsets. MPPs and CDPs are amplified in vitro with Flt3 ligand, stem cell factor, hyper-IL-6 and insulin- like growth factor-1. The four-factor cocktail readily induces self-renewal of MPPs and their progression into CDPs and has no self-renewal activity on CDPs. The amplified CDPs respond to all known DC poietins and generate all lymphoid tissue DCs in vivo and in vitro. Additionally, in vitro CDPs recapitulate the cell surface marker and gene expression profile of in vivo CDPs and possess a DC-primed transcription profile. Transforming growth factor-β1 (TGF-β1) impacts on CDPs and directs their differentiation towards cDCs. Genome-wide gene expression profiling of TGF-β1-induced genes identified transcription factors, such as interferon regulatory factor-4 (IRF-4) and RelB, that are implicated as instructive factors for cDC subset specification. TGF-β1 also induced the transcription factor inhibitor of differentiation/DNA binding 2 (Id2) that suppresses pDC development. Thus, TGF-β1 directs CDP differentiation into cDC by inducing both cDC instructive factors and pDC inhibitory factors.


systematic_name: M7822
exact_source: GSE22432_3611_200_DN
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in amplified: multipotent progenitors versus common dendritic cell progenitors.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7826
exact_source: GSE22432_3613_200_UP
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cultured common dendritic cell progenitors: untreated versus TGFB1 [GeneID=7040] for 4h.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7828
exact_source: GSE22432_3613_200_DN
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cultured common dendritic cell progenitors: untreated versus TGFB1 [GeneID=7040] for 4h.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7829
exact_source: GSE22432_3616_200_DN
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in amplified multipotent progenitors versus cultured untreated common dendritic cell progenitors.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7832
exact_source: GSE22432_3616_200_UP
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in amplified multipotent progenitors versus cultured untreated common dendritic cell progenitors.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7833
exact_source: GSE22432_3619_200_DN
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells: plasmacytoid versus cultured common progenitors treated by TGFB1 [GeneID=7040] for 4h.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7835
exact_source: GSE22432_3619_200_UP
source_species_code: MM
GEO_id: GSE22432
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cells: plasmacytoid versus cultured common progenitors treated by TGFB1 [GeneID=7040] for 4h.

description_full:
[cell repeats an earlier one in this file: 1480 characters]


systematic_name: M7836
exact_source: GSE22919_2501_200_DN
source_species_code: HS
GEO_id: GSE22919
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in NK cells: fresh versus stimulated with IL2 [GeneID=3558], IL-12 and IL15 [GeneID=3600].

description_full:
  We used Affymetrix expression arrays to determine changes in gene expression associated with activation of human NK cells mediated through treatment with cytokines IL-2, IL-12 and IL-18 over a 24 hour period.


systematic_name: M7837
exact_source: GSE22919_2501_200_UP
source_species_code: HS
GEO_id: GSE22919
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in NK cells: fresh versus stimulated with IL2 [GeneID=3558], IL-12 and IL15 [GeneID=3600].

description_full:
  We used Affymetrix expression arrays to determine changes in gene expression associated with activation of human NK cells mediated through treatment with cytokines IL-2, IL-12 and IL-18 over a 24 hour period.


description_brief: Genes up-regulated in resting T reg versus T conv cells.
systematic_name: M7839
exact_source: GSE24210_2706_200_UP
source_species_code: MM
GEO_id: GSE24210
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Regulatory T cells (Tregs) play a critical role in the maintenance of immunological self-tolerance. Naïve human or murine T cell treatment with the inhibitory cytokine IL35 induces a regulatory population, termed iTR35, that mediates suppression via IL35, but not IL10 or TGFβ, neither express nor require Foxp3, are strongly suppressive in five in vivo models, and exhibit in vivo stability. Treg-mediated suppression induces iTR35 generation in an IL35- and IL10-dependent manner in vitro, and in inflammatory conditions in vivo in Trichuris-infected intestines and within the tumor microenvironment, where they appear to contribute to the regulatory milieu. iTR35 may constitute a key mediator of infectious tolerance and may contribute to Treg-mediated tumor progression, and ex vivo-generated iTR35 may possess therapeutic utility.


description_brief: Genes up-regulated in CD4 [GeneID=920] T cells: untreated versus IL6 and TGFB1 [GeneID=3569;7040].
systematic_name: M7852
exact_source: GSE23505_2886_200_UP
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity1-4. Crucial for T helper17 (Th17) cells in vivo5,6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification7-10. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet. T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies.


systematic_name: M7853
exact_source: GSE23505_2885_200_DN
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated versus IL1B, IL6 [GeneID=3553;3569] and IL-23.

description_full:
  CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity1-4. Crucial for T helper17 (Th17) cells in vivo5,6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification7-10. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet. T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies.


systematic_name: M7856
exact_source: GSE23505_2885_200_UP
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated versus IL1B, IL6 [GeneID=3553;3569] and IL-23.

description_full:
  CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity1-4. Crucial for T helper17 (Th17) cells in vivo5,6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification7-10. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet. T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies.


systematic_name: M7859
exact_source: GSE23505_2887_200_DN
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with IL1B and IL6 [GeneID=3553;3569] versus those also treated with IL-23.

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7861
exact_source: GSE23505_2888_200_DN
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells treated with IL1B and IL6 [GeneID=3553;3569] versus those also treated with TGFB1 [GeneID=7040].

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7864
exact_source: GSE23505_2889_200_UP
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: IL1B, IL6 [GeneID=3553;3569] and IL-23 versus IL1B, IL6 and TGFB1 [GeneID=3553;3569;7040].

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7865
exact_source: GSE23505_2889_200_DN
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: IL1B, IL6 [GeneID=3553;3569] and IL-23 versus IL1B, IL6 and TGFB1 [GeneID=3553;3569;7040].

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7868
exact_source: GSE23505_2886_200_DN
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated versus IL6 and TGFB1 [GeneID=3569;7040].

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7869
exact_source: GSE23505_2887_200_UP
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with IL1B and IL6 [GeneID=3553;3569] versus those also treated with IL-23.

description_full:
[cell repeats an earlier one in this file: 1284 characters]


systematic_name: M7872
exact_source: GSE23505_2888_200_UP
source_species_code: MM
GEO_id: GSE23505
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells treated with IL1B and IL6 [GeneID=3553;3569] versus those also treated with TGFB1 [GeneID=7040].

description_full:
[cell repeats an earlier one in this file: 1284 characters]


description_brief: Genes down-regulated in macrophages: LYVE1+ [GeneID=10894] versus LYVE1- [GeneID=10894].
systematic_name: M7873
exact_source: GSE24492_3196_200_DN
source_species_code: MM
GEO_id: GSE24492
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  LYVE-1-positive macrophages were observed to be closely spatially associated with the developing lymphatic vasculature. The role of this population of macrophages in the embryo is uncharacterised. We used microarray analyses to investigate which genes are differentially regulated between LYVE-1-positive and LYVE-1-negative macrophages


description_brief: Genes up-regulated in B cells: light versus dark zone.
systematic_name: M7877
exact_source: GSE23925_2253_200_UP
source_species_code: MM
GEO_id: GSE23925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Microarrays of gene expression in mouse germinal center B cells photoactivated in the light zone or dark zone, and of naïve cells for comparison. We used microarray data to identify genes differentially expressed by B cells in the light and dark zones of the germinal center.


systematic_name: M7886
exact_source: GSE16385_2266_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes (12h) versus macrophages (12h) treated with rosiglitazone [PubChem=77999].

description_full:
  Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 4, 12, 24, 72 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml) or classically with interferon-gamma (IFNg 100 ng/ml)+tumor necrosis factor (TNF 50 ng/ml) or left without activation. Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1mM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.


systematic_name: M7889
exact_source: GSE16385_2267_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): control versus IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999].

description_full:
  Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 4, 12, 24, 72 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml) or classically with interferon-gamma (IFNg 100 ng/ml)+tumor necrosis factor (TNF 50 ng/ml) or left without activation. Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1mM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.


systematic_name: M7891
exact_source: GSE16385_2267_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): control versus IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999].

description_full:
  Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 4, 12, 24, 72 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml) or classically with interferon-gamma (IFNg 100 ng/ml)+tumor necrosis factor (TNF 50 ng/ml) or left without activation. Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1mM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.


systematic_name: M7892
exact_source: GSE16385_2274_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7894
exact_source: GSE16385_2273_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7896
exact_source: GSE16385_2273_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7898
exact_source: GSE16385_2263_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes (12h) versus macrophages (12h) treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7900
exact_source: GSE16385_2263_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes (12h) versus macrophages (12h) treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7902
exact_source: GSE16385_2262_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes (12h) versus macrophages (12h) treated with IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7905
exact_source: GSE16385_2266_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes (12h) versus macrophages (12h) treated with rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7906
exact_source: GSE25123_2325_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages: control versus treated with rosiglitazone [PubChem=77999].

description_full:
  Conditional macrophage-specific PPARg knockout mice were generated on C57Bl/6 background by breeding PPARg fl/- (one allele is floxed, the other is null) and lysozyme Cre transgenic mice. PPARg and IL-4 signaling was analyzed on bone marrow-derived macrophages. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and fresh media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7907
exact_source: GSE25123_2325_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages: control versus treated with rosiglitazone [PubChem=77999].

description_full:
  Conditional macrophage-specific PPARg knockout mice were generated on C57Bl/6 background by breeding PPARg fl/- (one allele is floxed, the other is null) and lysozyme Cre transgenic mice. PPARg and IL-4 signaling was analyzed on bone marrow-derived macrophages. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and fresh media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7908
exact_source: GSE25123_2326_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages: control versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
  Conditional macrophage-specific PPARg knockout mice were generated on C57Bl/6 background by breeding PPARg fl/- (one allele is floxed, the other is null) and lysozyme Cre transgenic mice. PPARg and IL-4 signaling was analyzed on bone marrow-derived macrophages. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and fresh media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7909
exact_source: GSE25123_2326_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages: control versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7911
exact_source: GSE16385_2268_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): control versus rosiglitazone [PubChem=77999] and IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7913
exact_source: GSE16385_2268_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): control versus rosiglitazone [PubChem=77999] and IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7915
exact_source: GSE16385_2262_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes (12h) versus macrophages (12h) treated with IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7916
exact_source: GSE16386_2260_200_DN
source_species_code: HS
GEO_id: GSE16386
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (6h): IL4 [GeneID=3565] versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
  Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 6 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml). Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1uM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.


systematic_name: M7917
exact_source: GSE16385_2264_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocytes (12h) versus macrophages (12h) treated with IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7920
exact_source: GSE16385_2264_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocytes (12h) versus macrophages (12h) treated with IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7921
exact_source: GSE25123_2323_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999]: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7922
exact_source: GSE25123_2324_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages: control versus treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7924
exact_source: GSE25123_2324_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages: control versus treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7925
exact_source: GSE16385_2272_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus rosiglitazone [PubChem=77999] and IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7926
exact_source: GSE25088_2292_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages: control versus treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
  C57Bl/6 wild-type and STAT6 KO mice were used to study PPARg and IL-4 signaling. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and frech media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7929
exact_source: GSE25088_2292_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages: control versus treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
  C57Bl/6 wild-type and STAT6 KO mice were used to study PPARg and IL-4 signaling. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and frech media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7930
exact_source: GSE25088_2293_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with IL4 [GeneID=3565].

description_full:
  C57Bl/6 wild-type and STAT6 KO mice were used to study PPARg and IL-4 signaling. Bone marrow of 3 mice per group was isolated and differentiated to macrophages with M-CSF (20 ng/ml). 20 ng/ml IL-4 was used to induce alternative macrophage activation and 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF, 2. M-CSF+RSG, 3. IL-4 and 4. IL-4+RSG. All compounds were added throughout the whole differentiation process, and frech media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 10 days, RNA was isolated and gene expression profiles were analyzed using Mouse Genome 430 2.0 microarrays from Affymetrix.


systematic_name: M7931
exact_source: GSE25088_2293_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7932
exact_source: GSE25088_2294_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7938
exact_source: GSE25123_2322_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: wildtype versus PPARG [GeneID=5468].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7939
exact_source: GSE25123_2323_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999]: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7943
exact_source: GSE16385_2272_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus rosiglitazone [PubChem=77999] and IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7944
exact_source: GSE25088_2301_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7947
exact_source: GSE25088_2301_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7948
exact_source: GSE25088_2302_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7950
exact_source: GSE25088_2302_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7951
exact_source: GSE25123_2320_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7953
exact_source: GSE25123_2320_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7954
exact_source: GSE25123_2321_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565]: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7958
exact_source: GSE25123_2321_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565]: wildtype versus PPARG [GeneID=5468] knockout.

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7961
exact_source: GSE25123_2329_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7962
exact_source: GSE25123_2333_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7965
exact_source: GSE25123_2333_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7967
exact_source: GSE25123_2334_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in wildtype bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7969
exact_source: GSE25123_2334_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in wildtype bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7971
exact_source: GSE25123_2335_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7972
exact_source: GSE25123_2335_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout treated with IL4 [GeneID=3565]: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7973
exact_source: GSE25088_2286_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7975
exact_source: GSE25123_2327_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7976
exact_source: GSE25123_2327_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7977
exact_source: GSE25123_2328_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7978
exact_source: GSE25123_2322_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: wildtype versus PPARG [GeneID=5468].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7980
exact_source: GSE25123_2329_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7986
exact_source: GSE16385_2278_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7989
exact_source: GSE16385_2278_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7991
exact_source: GSE25123_2336_200_UP
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7992
exact_source: GSE25123_2336_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout treated with rosiglitazone [PubChem=77999]: control versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M7993
exact_source: GSE16385_2274_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M7996
exact_source: GSE25088_2294_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M7998
exact_source: GSE25123_2328_200_DN
source_species_code: MM
GEO_id: GSE25123
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with PPARG [GeneID=5468] knockout: control versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 879 characters]


systematic_name: M8000
exact_source: GSE16386_2260_200_UP
source_species_code: HS
GEO_id: GSE16386
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (6h): IL4 [GeneID=3565] versus IL4 [GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
  Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 6 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml). Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1uM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.


systematic_name: M8001
exact_source: GSE25088_2288_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8002
exact_source: GSE25088_2289_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8003
exact_source: GSE25088_2289_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565] and rosiglitazone [PubChem=77999]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8011
exact_source: GSE16385_2279_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG and TNF [GeneID=3458;7124] versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8012
exact_source: GSE16385_2280_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): IFNG and TNF [GeneID=3458;7124] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8016
exact_source: GSE16385_2280_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG and TNF [GeneID=3458;7124] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8019
exact_source: GSE25088_2288_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with rosiglitazone [PubChem=77999]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8021
exact_source: GSE16385_2275_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8022
exact_source: GSE25088_2295_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with IL4[GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8024
exact_source: GSE25088_2295_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with STAT6 [GeneID=6778] knockout: control versus treated with IL4[GeneID=3565] and rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8025
exact_source: GSE16385_2276_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8026
exact_source: GSE16385_2277_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8027
exact_source: GSE16385_2277_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8028
exact_source: GSE25088_2287_200_UP
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8029
exact_source: GSE25088_2287_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages treated with IL4 [GeneID=3565]: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8030
exact_source: GSE16385_2276_200_UP
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages (12h): rosiglitazone [PubChem=77999] and IL4 [GeneID=3565] versus IFNG and TNF [GeneID=3458;7124].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8031
exact_source: GSE25088_2286_200_DN
source_species_code: MM
GEO_id: GSE25088
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages: wildtype versus STAT6 [GeneID=6778] knockout.

description_full:
[cell repeats an earlier one in this file: 698 characters]


systematic_name: M8032
exact_source: GSE16385_2275_200_DN
source_species_code: HS
GEO_id: GSE16385
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages (12h): IFNG, TNF [GeneID=3458;7124] and rosiglitazone [PubChem=77999] versus rosiglitazone [PubChem=77999].

description_full:
[cell repeats an earlier one in this file: 566 characters]


systematic_name: M8033
exact_source: GSE17301_3430_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells activated by anti-CD3 and anti-CD28 versus those stimulated by IFNA5 [GeneID=3442].

description_full:
  IFN alpha mediated gene expression pattern. The effect of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. This analysis examined the effects of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. Magnetically sorted untouched CD8+CD45R0- T cells from three different donors were unstimulated or stimulated with IFNa2b or with anti-CD3/CD28 Beads alone or along with IFNa2b or IFNa5 for 48 hours. Individual mRNA samples were analyzed using HG-U133A 2.0 array gene chips.


systematic_name: M8035
exact_source: GSE17301_3429_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells activated by anti-CD3 and anti-CD28 versus those stimulated by IFNA2 [GeneID=3440].

description_full:
  IFN alpha mediated gene expression pattern. The effect of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. This analysis examined the effects of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. Magnetically sorted untouched CD8+CD45R0- T cells from three different donors were unstimulated or stimulated with IFNa2b or with anti-CD3/CD28 Beads alone or along with IFNa2b or IFNa5 for 48 hours. Individual mRNA samples were analyzed using HG-U133A 2.0 array gene chips.


systematic_name: M8036
exact_source: GSE17301_3431_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells stimulated by IFNA2 [GeneID=3440] versus CD8 T cells stimulated by IFNA5 [GeneID=3442] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8037
exact_source: GSE17301_3431_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells stimulated by IFNA2 [GeneID=3440] versus CD8 T cells stimulated by IFNA5 [GeneID=3442] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8039
exact_source: GSE17301_3426_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells: control versus stimulated by IFNA2 [GeneID=3440] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8040
exact_source: GSE17301_3429_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells activated by anti-CD3 and anti-CD28 versus those stimulated by IFNA2 [GeneID=3440].

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8041
exact_source: GSE17301_3430_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells activated by anti-CD3 and anti-CD28 versus those stimulated by IFNA5 [GeneID=3442].

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8042
exact_source: GSE17301_3428_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells stimulated by IFNA2 [GeneID=3440] versus those activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8044
exact_source: GSE17301_3428_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells stimulated by IFNA2 [GeneID=3440] versus those activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8048
exact_source: GSE17301_3427_200_DN
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells: control versus stimulated by IFNA5 [GeneID=3442] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8049
exact_source: GSE17301_3426_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells: control versus stimulated by IFNA2 [GeneID=3440] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8050
exact_source: GSE17301_3427_200_UP
source_species_code: HS
GEO_id: GSE17301
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells: control versus stimulated by IFNA5 [GeneID=3442] and activated by anti-CD3 and anti-CD28.

description_full:
[cell repeats an earlier one in this file: 690 characters]


systematic_name: M8051
exact_source: GSE23984_3463_200_UP
source_species_code: HS
GEO_id: GSE23984
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in T cells: control versus TX527 (hypocalemic analog of 25-hydroxyvitamin D3 [PubChem=1593]).

description_full:
  Hypocalcemic vitamin D analogs are appealing molecules to exploit the immunomodulatory actions of active vitamin D in vivo. The functional modulation of dendritic cells is regarded as the key mechanism underlying their ability to regulate T cell responses. In contrast, the direct actions of vitamin D and structural analogs on T lymphocytes remain less well characterized. Microarray analysis was performed to gain insight into the direct immunomodulatory actions of TX527, a hypocalcemic vitamin D analog, on human T lymphocytes. Gene expression analysis revealed that TX527 regulated a wide variety of genes involved in different aspects of T cell function, including cellular growth and proliferation, cell death, cellular development, cellular movement and cell-to-cell signalling and interaction.


systematic_name: M8052
exact_source: GSE23984_3463_200_DN
source_species_code: HS
GEO_id: GSE23984
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in T cells: control versus TX527 (hypocalemic analog of 25-hydroxyvitamin D3 [PubChem=1593]).

description_full:
  Hypocalcemic vitamin D analogs are appealing molecules to exploit the immunomodulatory actions of active vitamin D in vivo. The functional modulation of dendritic cells is regarded as the key mechanism underlying their ability to regulate T cell responses. In contrast, the direct actions of vitamin D and structural analogs on T lymphocytes remain less well characterized. Microarray analysis was performed to gain insight into the direct immunomodulatory actions of TX527, a hypocalcemic vitamin D analog, on human T lymphocytes. Gene expression analysis revealed that TX527 regulated a wide variety of genes involved in different aspects of T cell function, including cellular growth and proliferation, cell death, cellular development, cellular movement and cell-to-cell signalling and interaction.


description_brief: Genes up-regulated in macrophages: wildtype versus PPARG [GeneID=5468] knockout.
systematic_name: M8053
exact_source: GSE24292_2713_200_UP
source_species_code: MM
GEO_id: GSE24292
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  PPARg is a nuclear receptor that plays an important role in lipid metabolism, homeostasis and immunity. Microarray analysis of gene expression was performed in macrophages from WT and PPARg KO mice. Differentially expressed genes were selected for further analysis.


systematic_name: M8056
exact_source: GSE24726_2454_200_DN
source_species_code: MM
GEO_id: GSE24726
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (6 days after knockout): wildtype versus TCF4 [GeneID=6925] knockout.

description_full:
  The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the “default” cDC fate, in part through direct regulation of lineage-specific gene expression programs.


systematic_name: M8058
exact_source: GSE24726_2453_200_DN
source_species_code: MM
GEO_id: GSE24726
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in plasmacytoid dendritic cells (4 days after knockout): wildtype versus TCF4 [GeneID=6925] knockout.

description_full:
  The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the “default” cDC fate, in part through direct regulation of lineage-specific gene expression programs.


systematic_name: M8063
exact_source: GSE24726_2454_200_UP
source_species_code: MM
GEO_id: GSE24726
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (6 days after knockout): wildtype versus TCF4 [GeneID=6925] knockout.

description_full:
[cell repeats an earlier one in this file: 996 characters]


systematic_name: M8064
exact_source: GSE24726_2453_200_UP
source_species_code: MM
GEO_id: GSE24726
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in plasmacytoid dendritic cells (4 days after knockout): wildtype versus TCF4 [GeneID=6925] knockout.

description_full:
[cell repeats an earlier one in this file: 996 characters]


description_brief: Genes down-regulated in myeloid dendritic cells: hypoxia versus normoxia.
systematic_name: M8065
exact_source: GSE22282_3498_200_DN
source_species_code: HS
GEO_id: GSE22282
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Dendritic cells (DCs) are professional antigen-presenting cells whose activity is intrinsically linked to the microenvironment. Hypoxia is a condition of low oxygen tension occurring in inflammatory tissues that creates a special microenvironment conditioning cell physiology. We studied the effects of hypoxia on the differentiation of human monocytes into DCs and maturation into mature DCs. Mature DCs were differentiated in vitro from human monocytes under normoxic or hypoxic conditions and the gene expression profile was determined.


description_brief: Genes down-regulated in thymic implants from fetal liver versus those from adult bone marrow.
systematic_name: M8069
exact_source: GSE25085_2626_200_DN
source_species_code: HS
GEO_id: GSE25085
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Human fetal and adult hematopoietic stem cells (HSC) were obtained from fetal liver, fetal bone marrow (BM), and adult BM. These were injected into human fetal thymic implants in SCID-hu Thy/Liv mice (4-6 separate mice per HSC donor) and allowed to mature into single positive CD4+ (SP4) thymocytes over the course of 7-8 weeks. SP4 thymocytes from injected stem cells were subsequently sort-purified from thymic implants and gene expression was performed.


systematic_name: M8079
exact_source: GSE23398_3081_200_DN
source_species_code: MM
GEO_id: GSE23398
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymph node CD4 [GeneID=920] T cells: scurfy (non-functional form of FOXP3 [GeneID=50943]) versus scurfy and IL2 [GeneID=3558] knockout.

description_full:
  The goal of the study was to identify the genes which are regulated by Interleukin-2 in the CD4+ T cells of the scurfy mice during regulatory T-cell deficiency. Scurfy (Sf) mice bear a mutation in the forkhead box P3 (Foxp3) transcription factor, lack regulatory T-cells (Treg), develop multi-organ inflammation, and die prematurely. The major target organs affected are skin, lungs, and liver. Sf mice lacking the Il2 gene (Sf.Il2-/-), despite devoid of Treg, did not develop skin and lung inflammation, but the inflammation in liver, pancreas, submandibular gland and colon remained. Genome-wide microarray analysis revealed hundreds of genes were differentially regulated among Sf, Sf.Il2-/-, and B6 CD4+ T-cells but the most changes were those encoding receptors for trafficking/chemotaxis/retention and lymphokines. Our study suggests that IL-2 controls the skin and lung inflammation in Sf mice in an apparent \organ-specific\ manner through two novel mechanisms: by regulating the expression of genes encoding receptors for T-cell trafficking/chemotaxis/retention and by regulating Th2 cell expansion and lymphokine production. Thus, IL-2 is a master regulator for multi-organ inflammation and an underlying etiological factor for various diseases associated with skin and lung inflammation. Methods: CD4+ T cells were purified by Fluorescence Assisted Cell Sorting from the peripheral lymph nodes of (A) three individual Scurfy (Sf; B6.Cg-Foxp3sf/J) male mice, (B) three individual Sf.Il2-/- male mice (Scurfy mice carrying a null Interleukin (IL)-2 gene (B6.129P2-Il2tm1Hor/J)) and (C) a pooled sample of lymph nodes from two B6 (C57BL/6J) mice. All the mice were 3 weeks old. Total RNA was prepared using RNeasy mini kit (Qiagen). RNA samples were converted to cRNA, labeled and hybridized to Affymetrix Mouse 430_2 chips (Mouse Genome 430 2.0 Array, Affymetrix, Santa Clara, CA) at the University of Virginia DNA Sciences Core Facility.


systematic_name: M8080
exact_source: GSE23398_3081_200_UP
source_species_code: MM
GEO_id: GSE23398
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymph node CD4 [GeneID=920] T cells: scurfy (non-functional form of FOXP3 [GeneID=50943]) versus scurfy and IL2 [GeneID=3558] knockout.

description_full:
  The goal of the study was to identify the genes which are regulated by Interleukin-2 in the CD4+ T cells of the scurfy mice during regulatory T-cell deficiency. Scurfy (Sf) mice bear a mutation in the forkhead box P3 (Foxp3) transcription factor, lack regulatory T-cells (Treg), develop multi-organ inflammation, and die prematurely. The major target organs affected are skin, lungs, and liver. Sf mice lacking the Il2 gene (Sf.Il2-/-), despite devoid of Treg, did not develop skin and lung inflammation, but the inflammation in liver, pancreas, submandibular gland and colon remained. Genome-wide microarray analysis revealed hundreds of genes were differentially regulated among Sf, Sf.Il2-/-, and B6 CD4+ T-cells but the most changes were those encoding receptors for trafficking/chemotaxis/retention and lymphokines. Our study suggests that IL-2 controls the skin and lung inflammation in Sf mice in an apparent \organ-specific\ manner through two novel mechanisms: by regulating the expression of genes encoding receptors for T-cell trafficking/chemotaxis/retention and by regulating Th2 cell expansion and lymphokine production. Thus, IL-2 is a master regulator for multi-organ inflammation and an underlying etiological factor for various diseases associated with skin and lung inflammation. Methods: CD4+ T cells were purified by Fluorescence Assisted Cell Sorting from the peripheral lymph nodes of (A) three individual Scurfy (Sf; B6.Cg-Foxp3sf/J) male mice, (B) three individual Sf.Il2-/- male mice (Scurfy mice carrying a null Interleukin (IL)-2 gene (B6.129P2-Il2tm1Hor/J)) and (C) a pooled sample of lymph nodes from two B6 (C57BL/6J) mice. All the mice were 3 weeks old. Total RNA was prepared using RNeasy mini kit (Qiagen). RNA samples were converted to cRNA, labeled and hybridized to Affymetrix Mouse 430_2 chips (Mouse Genome 430 2.0 Array, Affymetrix, Santa Clara, CA) at the University of Virginia DNA Sciences Core Facility.


systematic_name: M8081
exact_source: GSE23502_2654_200_DN
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in myeloid-derived suppressor cells with HDC [GeneID=3067] knockout: bone marrow versus colon tumor.

description_full:
  Differentially expressed genes of CD11b+Gr-1+ immature myeloid cells (IMCs) in the bone marrow and colonic tumor setting of histidine decarboxylase (HDC)-KO mice were examined by microarray (Affymetrix Mouse 430.2 array). Myeloid differentiation-related candidate genes were sought to be isolated and functionally studied.


systematic_name: M8082
exact_source: GSE23502_2654_200_UP
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in myeloid-derived suppressor cells with HDC [GeneID=3067] knockout: bone marrow versus colon tumor.

description_full:
  Differentially expressed genes of CD11b+Gr-1+ immature myeloid cells (IMCs) in the bone marrow and colonic tumor setting of histidine decarboxylase (HDC)-KO mice were examined by microarray (Affymetrix Mouse 430.2 array). Myeloid differentiation-related candidate genes were sought to be isolated and functionally studied.


systematic_name: M8085
exact_source: GSE23502_2652_200_UP
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in myeloid-derived suppressor cells from colon tumors: wildtype versus HDC [GeneID=3067] knockout.

description_full:
  Differentially expressed genes of CD11b+Gr-1+ immature myeloid cells (IMCs) in the bone marrow and colonic tumor setting of histidine decarboxylase (HDC)-KO mice were examined by microarray (Affymetrix Mouse 430.2 array). Myeloid differentiation-related candidate genes were sought to be isolated and functionally studied.


systematic_name: M8086
exact_source: GSE23502_2652_200_DN
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in myeloid-derived suppressor cells from colon tumors: wildtype versus HDC [GeneID=3067] knockout.

description_full:
[cell repeats an earlier one in this file: 322 characters]


systematic_name: M8089
exact_source: GSE23502_2651_200_DN
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in myeloid-derived suppressor cells from bone marrow: wildtype versus HDC [GeneID=3067] knockout.

description_full:
[cell repeats an earlier one in this file: 322 characters]


systematic_name: M8090
exact_source: GSE23502_2651_200_UP
source_species_code: MM
GEO_id: GSE23502
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in myeloid-derived suppressor cells from bone marrow: wildtype versus HDC [GeneID=3067] knockout.

description_full:
[cell repeats an earlier one in this file: 322 characters]


description_brief: Genes up-regulated in spleen follicular B lymphocytes: wildtype versus IRF8 [GeneID=3394] knockout.
systematic_name: M8092
exact_source: GSE24972_2963_200_UP
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Conditional IRF8 KO mice (mice with a conditional allele of Irf8 crossed with CD19-Cre mice) showed increased numbers of both Gene expression data spleen marginal zone (MZ) and Gene expression data spleen follicular (FO) B cells compared to control mice. To evaluate gene expression patterns that distinguished FO or MZ B cells derived from conditional KO and control mice, we used Affymetrix GeneChip® Mouse gene 1.0 ST Array.


systematic_name: M8093
exact_source: GSE24972_2965_200_DN
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen B lymphocytes with IRF8 [GeneID=3394] knockout: marginal zone versus follicular.

description_full:
  Conditional IRF8 KO mice (mice with a conditional allele of Irf8 crossed with CD19-Cre mice) showed increased numbers of both Gene expression data spleen marginal zone (MZ) and Gene expression data spleen follicular (FO) B cells compared to control mice. To evaluate gene expression patterns that distinguished FO or MZ B cells derived from conditional KO and control mice, we used Affymetrix GeneChip® Mouse gene 1.0 ST Array.


systematic_name: M8094
exact_source: GSE24972_2962_200_DN
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen marginal zone B lymphocytes: wildtype versus IRF8 [GeneID=3394] knockout.

description_full:
  Conditional IRF8 KO mice (mice with a conditional allele of Irf8 crossed with CD19-Cre mice) showed increased numbers of both Gene expression data spleen marginal zone (MZ) and Gene expression data spleen follicular (FO) B cells compared to control mice. To evaluate gene expression patterns that distinguished FO or MZ B cells derived from conditional KO and control mice, we used Affymetrix GeneChip® Mouse gene 1.0 ST Array.


systematic_name: M8096
exact_source: GSE24972_2963_200_DN
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen follicular B lymphocytes: wildtype versus IRF8 [GeneID=3394] knockout.

description_full:
[cell repeats an earlier one in this file: 427 characters]


systematic_name: M8097
exact_source: GSE24972_2962_200_UP
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleen marginal zone B lymphocytes: wildtype versus IRF8 [GeneID=3394] knockout.

description_full:
[cell repeats an earlier one in this file: 427 characters]


systematic_name: M8099
exact_source: GSE24972_2965_200_UP
source_species_code: MM
GEO_id: GSE24972
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleen B lymphocytes with IRF8 [GeneID=3394] knockout: marginal zone versus follicular.

description_full:
[cell repeats an earlier one in this file: 427 characters]


systematic_name: M8100
exact_source: GSE19941_3671_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in NFKB1 and IL10 [GeneID=4790;3586] knockout macrophages stimulated by LPS versus those also stimulated by IL10 [GeneID=3586].

description_full:
  Bone marrow-derived macrophages were produced from mice lacking IL-10 alone (IL10-def) or mice lacking both IL-10 and the p50/p105 subunit of NF-kB (p50/IL10), and left unstimulated, stimulated with LPS (1 ng/ml) or stimulated with LPS and IL-10 (0.3 ng/ml).


systematic_name: M8102
exact_source: GSE19941_3664_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages stimulated by LPS: IL10 [GeneID=3586] knockout versus IL10 and NFKB1 [GeneID=3586;4790] knockout.

description_full:
  Bone marrow-derived macrophages were produced from mice lacking IL-10 alone (IL10-def) or mice lacking both IL-10 and the p50/p105 subunit of NF-kB (p50/IL10), and left unstimulated, stimulated with LPS (1 ng/ml) or stimulated with LPS and IL-10 (0.3 ng/ml).


systematic_name: M8103
exact_source: GSE19941_3668_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in unstimulated IL10 [GeneID=3586] knockout macrophages versus NFKB1 and IL10 [GeneID=4790;3586] knockout macrophages stimulated by LPS.

description_full:
  Bone marrow-derived macrophages were produced from mice lacking IL-10 alone (IL10-def) or mice lacking both IL-10 and the p50/p105 subunit of NF-kB (p50/IL10), and left unstimulated, stimulated with LPS (1 ng/ml) or stimulated with LPS and IL-10 (0.3 ng/ml).


systematic_name: M8107
exact_source: GSE19941_3667_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IL10 [GeneID=3586] knockout macrophages: unstimulated versus stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8109
exact_source: GSE19941_3667_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IL10 [GeneID=3586] knockout macrophages: unstimulated versus stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8110
exact_source: GSE19941_3663_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in unstimulated macrophages: IL10 [GeneID=3586] knockout versus NFKB1 [GeneID=4790] knockout.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8111
exact_source: GSE19941_3668_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in unstimulated IL10 [GeneID=3586] knockout macrophages versus NFKB1 and IL10 [GeneID=4790;3586] knockout macrophages stimulated by LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8112
exact_source: GSE19941_3663_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in unstimulated macrophages: IL10 [GeneID=3586] knockout versus NFKB1 [GeneID=4790] knockout.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8113
exact_source: GSE19941_3669_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IL10 and NFKB1 [GeneID=4790;3586] knockout macrophages: unstimulated versus stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8115
exact_source: GSE19941_3665_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IL10 [GeneID=3586] knockout macrophages stimulated by IL10 [GeneID=3586] versus NFKB1 [GeneID=4790] knockout macrophages stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8117
exact_source: GSE19941_3664_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages stimulated by LPS: IL10 [GeneID=3586] knockout versus IL10 and NFKB1 [GeneID=3586;4790] knockout.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8119
exact_source: GSE19941_3671_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in NFKB1 and IL10 [GeneID=4790;3586] knockout macrophages stimulated by LPS versus those also stimulated by IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8120
exact_source: GSE19941_3669_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IL10 and NFKB1 [GeneID=4790;3586] knockout macrophages: unstimulated versus stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8121
exact_source: GSE19941_3665_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IL10 [GeneID=3586] knockout macrophages stimulated by IL10 [GeneID=3586] versus NFKB1 [GeneID=4790] knockout macrophages stimulated by IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8125
exact_source: GSE19941_3670_200_DN
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IL10 [GeneID=3586] knockout macrophages stimulated by LPS versus those also stimulated by IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 258 characters]


systematic_name: M8126
exact_source: GSE19941_3670_200_UP
source_species_code: MM
GEO_id: GSE19941
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IL10 [GeneID=3586] knockout macrophages stimulated by LPS versus those also stimulated by IL10 [GeneID=3586].

description_full:
[cell repeats an earlier one in this file: 258 characters]


description_brief: Genes up-regulated in AGS cells (gastric adenocarcinoma): control versus H. pylori LPS.
systematic_name: M8127
exact_source: GSE25146_3045_200_UP
source_species_code: HS
GEO_id: GSE25146
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  This study set out to identify global changes in gene expression in AGS gastric epithelial cells following 8 hours stimulation with 10 μg/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori. Microarray analysis was used to compare changes in gene expression between cells treated with 10 μg/ml H. pylori LPS and untreated cells at the same time point.


description_brief: Genes down-regulated in MKN45 cells (stomach cancer): control versus H. pylori LPS.
systematic_name: M8128
exact_source: GSE25147_3046_200_DN
source_species_code: HS
GEO_id: GSE25147
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  This study set out to identify global changes in gene expression in MKN45 gastric epithelial cells following 8 hours stimulation with 10 μg/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori. Microarray analysis was used to compare changes in gene expression between cells treated with 10 μg/ml H. pylori LPS and untreated cells at the same time point.


description_brief: Genes up-regulated in decidual macrophages with ITGAX [GeneID=3687] high versus low.
systematic_name: M8131
exact_source: GSE22342_3044_200_UP
source_species_code: HS
GEO_id: GSE22342
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Decidual macrophage populations, CD11cHI and CD11cLO cells were analyzed for expression profiles and unique characteristics. We used microarrays to detail the global program of gene expression and to determine differences between these two unique decidual macrophage populations.


systematic_name: M8133
exact_source: GSE26290_2399_200_DN
source_species_code: MM
GEO_id: GSE26290
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cytotoxic T cells: control versus treated with Akt inhibitor VIII [PubChem=10196499].

description_full:
  In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1). The role of PDK1 and Akt in CTL has however not been fully defined. In order to explore the relative roles of these kinases in CTL we used microarrays to profile the gene expression of control and PDK1 null CTL. In separate experiments we compared the gene expression profiles of control and Akt inhibitor treated CTL.


systematic_name: M8135
exact_source: GSE26290_2399_200_UP
source_species_code: MM
GEO_id: GSE26290
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cytotoxic T cells: control versus treated with Akt inhibitor VIII [PubChem=10196499].

description_full:
  In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1). The role of PDK1 and Akt in CTL has however not been fully defined. In order to explore the relative roles of these kinases in CTL we used microarrays to profile the gene expression of control and PDK1 null CTL. In separate experiments we compared the gene expression profiles of control and Akt inhibitor treated CTL.


description_brief: Genes up-regulated in CD8 T cells: IL10+ [GeneID=3586] versus IL10- [GeneID=3586].
systematic_name: M8140
exact_source: GSE25846_2718_200_UP
source_species_code: MM
GEO_id: GSE25846
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  IL-10 is an anti-inflammatory cytokine that has been shown to be produced by antigen-specific CD8 T cells at the peak of viral encephalitis. We found that IL-10+CD8 T cells are more activated and cytolytic than IL-10-CD8 T cells. We used microarrays to detect gene expression changes in directly ex vivo sorted CNS IL-10+ and IL-10- CD8 T cells from a neurotropic J2.2-V-1-infected mouse.


description_brief: Genes down-regulated in neutrophils under hypoxia: EGLN3 [GeneID=112399] knockout versus wildtype.
systematic_name: M8143
exact_source: GSE26023_3381_200_DN
source_species_code: MM
GEO_id: GSE26023
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Neutrophils were isolated form peripheral blood of wildtype and Phd3 null mice, cultured for 4 hours in hypoxia (3% O2) and micro array analysis performed The aim of the present study is to identify the mechanism by which phd3 is required for the hypoxia mediated survival of neutrophils


