# gene_set_details

description_brief: Genes up-regulated in comparison of SP1 thymocytes versus SP2 thymocytes.
systematic_name: M5023
exact_source: GSE30083_2160_200_UP
source_species_code: MM
GEO_id: GSE30083
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  After positive selection in the thymus, the newly generated single positive (SP) thymocytes are phenotypically and functionally immature and undergo apoptosis upon antigen stimulation. In the thymic medullary microenvironment, SP cells progressively acquire immunocompetence. Negative selection to remove autoreactive T cells also occur at this stage. We have defined four subsets of CD4 SP, namely, SP1, SP2, SP3, and SP4 that follow a functional maturation program and a sequential emergence during mouse ontogeny.We used microarray to detail the global programm of gene expression during the maturation of murine CD4 single positive thymocytes


systematic_name: M5041
exact_source: GSE30962_1570_200_UP
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-acute infection versus splenic secondary CD8 effector T cells at day 8 post-acute infection.

description_full:
  Understanding the response of memory CD8 T cells to persistent antigen re-stimulation and the role of CD4 T cell help is critical to the design of successful vaccines for chronic diseases. However, studies comparing the protective abilities and qualities of memory and naïve cells have been mostly performed in acute infections, and little is known about their roles during chronic infections. Herein, we show that memory cells dominate over naïve cells and are protective when present in large enough numbers to quickly reduce infection. In contrast, when infection is not rapidly reduced, memory cells are quickly lost, unlike naïve cells. This loss of memory cells is due to (i) an early block in cell proliferation, (ii) selective regulation by the inhibitory receptor 2B4, and (iii) increased reliance on CD4 T cell help. These findings have important implications towards the design of T cell vaccines against chronic infections and tumors.


systematic_name: M5043
exact_source: GSE30962_1570_200_DN
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-acute infection versus splenic secondary CD8 effector T cells at day 8 post-acute infection.

description_full:
  Understanding the response of memory CD8 T cells to persistent antigen re-stimulation and the role of CD4 T cell help is critical to the design of successful vaccines for chronic diseases. However, studies comparing the protective abilities and qualities of memory and naïve cells have been mostly performed in acute infections, and little is known about their roles during chronic infections. Herein, we show that memory cells dominate over naïve cells and are protective when present in large enough numbers to quickly reduce infection. In contrast, when infection is not rapidly reduced, memory cells are quickly lost, unlike naïve cells. This loss of memory cells is due to (i) an early block in cell proliferation, (ii) selective regulation by the inhibitory receptor 2B4, and (iii) increased reliance on CD4 T cell help. These findings have important implications towards the design of T cell vaccines against chronic infections and tumors.


systematic_name: M5044
exact_source: GSE30962_1571_200_UP
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-chronic infection versus splenic secondary CD8 effector T cells at day 8 post-chronic infection.

description_full:
  Understanding the response of memory CD8 T cells to persistent antigen re-stimulation and the role of CD4 T cell help is critical to the design of successful vaccines for chronic diseases. However, studies comparing the protective abilities and qualities of memory and naïve cells have been mostly performed in acute infections, and little is known about their roles during chronic infections. Herein, we show that memory cells dominate over naïve cells and are protective when present in large enough numbers to quickly reduce infection. In contrast, when infection is not rapidly reduced, memory cells are quickly lost, unlike naïve cells. This loss of memory cells is due to (i) an early block in cell proliferation, (ii) selective regulation by the inhibitory receptor 2B4, and (iii) increased reliance on CD4 T cell help. These findings have important implications towards the design of T cell vaccines against chronic infections and tumors.


systematic_name: M5045
exact_source: GSE30962_1571_200_DN
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-chronic infection versus splenic secondary CD8 effector T cells at day 8 post-chronic infection.

description_full:
[cell repeats an earlier one in this file: 946 characters]


systematic_name: M5046
exact_source: GSE30962_1572_200_UP
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-acute infection versus splenic primary CD8 effector T cells at day 8 post-chronic infection.

description_full:
[cell repeats an earlier one in this file: 946 characters]


systematic_name: M5048
exact_source: GSE30962_1572_200_DN
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of splenic primary CD8 effector T cells at day 8 post-acute infection versus splenic primary CD8 effector T cells at day 8 post-chronic infection.

description_full:
[cell repeats an earlier one in this file: 946 characters]


systematic_name: M5049
exact_source: GSE30962_1573_200_UP
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of splenic secondary CD8 effector T cells at day 8 post-acute infection versus splenic secondary CD8 effector T cells at day 8 post-chronic infection.

description_full:
[cell repeats an earlier one in this file: 946 characters]


systematic_name: M5052
exact_source: GSE30962_1573_200_DN
source_species_code: MM
GEO_id: GSE30962
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of splenic secondary CD8 effector T cells at day 8 post-acute infection versus splenic secondary CD8 effector T cells at day 8 post-chronic infection.

description_full:
[cell repeats an earlier one in this file: 946 characters]


systematic_name: M5054
exact_source: GSE31082_2167_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4+ [GeneID=920] CD8+ thymocytes.

description_full:
  Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets.


systematic_name: M5055
exact_source: GSE31082_2167_200_DN
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4+ [GeneID=920] CD8+ thymocytes.

description_full:
  Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets.


systematic_name: M5057
exact_source: GSE31082_2168_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4+ [GeneID=920] CD8- thymocytes.

description_full:
  Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets.


systematic_name: M5059
exact_source: GSE31082_2168_200_DN
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4+ [GeneID=920] CD8- thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5061
exact_source: GSE31082_2169_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5063
exact_source: GSE31082_2169_200_DN
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4- [GeneID=920] CD8- thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5064
exact_source: GSE31082_2170_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4+ [GeneID=920] CD8+ thymocytes versus CD4+ [GeneID=920] CD8- thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5065
exact_source: GSE31082_2170_200_DN
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4+ [GeneID=920] CD8+ thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5066
exact_source: GSE31082_2171_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4+ [GeneID=920] CD8+ thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5069
exact_source: GSE31082_2172_200_UP
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4+ [GeneID=920] CD8- thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


systematic_name: M5070
exact_source: GSE31082_2172_200_DN
source_species_code: MM
GEO_id: GSE31082
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4+ [GeneID=920] CD8- thymocytes versus CD4- [GeneID=920] CD8+ thymocytes.

description_full:
[cell repeats an earlier one in this file: 783 characters]


description_brief: Genes up-regulated in comparison of memory CD8 T cells versus naive CD8 T cells.
systematic_name: M5072
exact_source: GSE32423_1395_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Effects of IL-4 on CD8 T cells functions are largely unknown. IL-4 induces survival and proliferation of CD8 T cells, but several studies suggest that IL-4 could also affect several functions of CD8 T cells such as cytotoxicity. Our team has shown that IL-4 repress the expression of Ccl5 in vitro. To define more precisely the impact of IL-4 on CD8 T cells, we performed a whole genome expression microarray analysis of naive and memory CD8 T cells cultured in presence or absence of IL-4. This approach allowed us to define the IL4-gene-expression signature on CD8 T cells.


systematic_name: M5074
exact_source: GSE32423_1396_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus naive CD8 T cells treated with IL7 [GeneID=3574].

description_full:
  Effects of IL-4 on CD8 T cells functions are largely unknown. IL-4 induces survival and proliferation of CD8 T cells, but several studies suggest that IL-4 could also affect several functions of CD8 T cells such as cytotoxicity. Our team has shown that IL-4 repress the expression of Ccl5 in vitro. To define more precisely the impact of IL-4 on CD8 T cells, we performed a whole genome expression microarray analysis of naive and memory CD8 T cells cultured in presence or absence of IL-4. This approach allowed us to define the IL4-gene-expression signature on CD8 T cells.


systematic_name: M5078
exact_source: GSE32423_1396_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus naive CD8 T cells treated with IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5079
exact_source: GSE32423_1397_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells treated with IL4 [GeneID=3565] and IL7 [GeneID=3574] versus naive CD8 T cells treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5081
exact_source: GSE32423_1397_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells treated with IL4 [GeneID=3565] and IL7 [GeneID=3574] versus naive CD8 T cells treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5083
exact_source: GSE32423_1398_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells versus those  treated with IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5084
exact_source: GSE32423_1398_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells versus those  treated with IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5085
exact_source: GSE32423_1399_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells versus those  treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5086
exact_source: GSE32423_1399_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells versus those  treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5087
exact_source: GSE32423_1400_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells versus those  treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5088
exact_source: GSE32423_1400_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells versus those  treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5089
exact_source: GSE32423_1401_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5092
exact_source: GSE32423_1401_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5093
exact_source: GSE32423_1402_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5094
exact_source: GSE32423_1402_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5095
exact_source: GSE32423_1403_200_UP
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of naive CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5096
exact_source: GSE32423_1403_200_DN
source_species_code: MM
GEO_id: GSE32423
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of naive CD8 T cells treated with IL7 [GeneID=3574] versus those treated with IL4 [GeneID=3565] and IL7 [GeneID=3574].

description_full:
[cell repeats an earlier one in this file: 575 characters]


systematic_name: M5097
exact_source: GSE3337_1053_200_UP
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD8+ dendritic cells (DC) at 4 h versus those treated with IFNG [GeneID=3458] at 4 h.

description_full:
  Although much is known on the transcriptional profiles of dendritic cells (DCs) during maturation, the molecular switches critical for the acquisition of a tolerogenic program by DCs are still obscure. In the present study, we explored the gene expression pattern of CD8+ DCs purified from the mouse spleen and treated with interferon (IFN)-gamma. The cytokine, indeed, potentiates the tolerogenic potential of this DC subset via induction of the immunosuppressive tryptophan catabolism mediated by indoleamine 2,3-dioxygenase (IDO). By comparing the expression of the IFN-gamma-modulated genes in IDO+ versus IDO- murine DCs, we found a consistent and selective association of the IDO-competent phenotype with the down-modulation of the Tyrobp gene, encoding the adapter molecule DAP12. IFN-gamma-mediated down-modulation of this gene involved IFN consensus sequence binding protein (ICSBP), a transcription factor also known as IRF-8. While silencing of Tyrobp conferred IDO functional competence on IDO- DCs, silencing of Icsbp1 in IDO+ cells completely abolished IDO expression and function. In parallel, silencing of TYROBP conferred IDO competence on human IDO- DCs while silencing of IRF8 impaired IDO expression and activity in human IDO+ DCs. Therefore, the same small set of molecular switches controls IDO competence in murine and human DCs.


systematic_name: M5099
exact_source: GSE3337_1053_200_DN
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD8+ dendritic cells (DC) at 4 h versus those treated with IFNG [GeneID=3458] at 4 h.

description_full:
  Although much is known on the transcriptional profiles of dendritic cells (DCs) during maturation, the molecular switches critical for the acquisition of a tolerogenic program by DCs are still obscure. In the present study, we explored the gene expression pattern of CD8+ DCs purified from the mouse spleen and treated with interferon (IFN)-gamma. The cytokine, indeed, potentiates the tolerogenic potential of this DC subset via induction of the immunosuppressive tryptophan catabolism mediated by indoleamine 2,3-dioxygenase (IDO). By comparing the expression of the IFN-gamma-modulated genes in IDO+ versus IDO- murine DCs, we found a consistent and selective association of the IDO-competent phenotype with the down-modulation of the Tyrobp gene, encoding the adapter molecule DAP12. IFN-gamma-mediated down-modulation of this gene involved IFN consensus sequence binding protein (ICSBP), a transcription factor also known as IRF-8. While silencing of Tyrobp conferred IDO functional competence on IDO- DCs, silencing of Icsbp1 in IDO+ cells completely abolished IDO expression and function. In parallel, silencing of TYROBP conferred IDO competence on human IDO- DCs while silencing of IRF8 impaired IDO expression and activity in human IDO+ DCs. Therefore, the same small set of molecular switches controls IDO competence in murine and human DCs.


systematic_name: M5100
exact_source: GSE3337_1054_200_UP
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD8+ dendritic cells (DC) at 16 h versus those treated with IFNG [GeneID=31658] at 16 h.

description_full:
  Although much is known on the transcriptional profiles of dendritic cells (DCs) during maturation, the molecular switches critical for the acquisition of a tolerogenic program by DCs are still obscure. In the present study, we explored the gene expression pattern of CD8+ DCs purified from the mouse spleen and treated with interferon (IFN)-gamma. The cytokine, indeed, potentiates the tolerogenic potential of this DC subset via induction of the immunosuppressive tryptophan catabolism mediated by indoleamine 2,3-dioxygenase (IDO). By comparing the expression of the IFN-gamma-modulated genes in IDO+ versus IDO- murine DCs, we found a consistent and selective association of the IDO-competent phenotype with the down-modulation of the Tyrobp gene, encoding the adapter molecule DAP12. IFN-gamma-mediated down-modulation of this gene involved IFN consensus sequence binding protein (ICSBP), a transcription factor also known as IRF-8. While silencing of Tyrobp conferred IDO functional competence on IDO- DCs, silencing of Icsbp1 in IDO+ cells completely abolished IDO expression and function. In parallel, silencing of TYROBP conferred IDO competence on human IDO- DCs while silencing of IRF8 impaired IDO expression and activity in human IDO+ DCs. Therefore, the same small set of molecular switches controls IDO competence in murine and human DCs.


systematic_name: M5101
exact_source: GSE3337_1054_200_DN
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD8+ dendritic cells (DC) at 16 h versus those treated with IFNG [GeneID=31658] at 16 h.

description_full:
[cell repeats an earlier one in this file: 1352 characters]


systematic_name: M5102
exact_source: GSE3337_1055_200_UP
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD8+ dendritic cells (DC) at 4 h versus those treated with IFNG [GeneID=3458] at 16 h.

description_full:
[cell repeats an earlier one in this file: 1352 characters]


systematic_name: M5104
exact_source: GSE3337_1055_200_DN
source_species_code: MM
GEO_id: GSE3337
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD8+ dendritic cells (DC) at 4 h versus those treated with IFNG [GeneID=3458] at 16 h.

description_full:
[cell repeats an earlier one in this file: 1352 characters]


systematic_name: M5105
exact_source: GSE33513_2166_200_UP
source_species_code: MM
GEO_id: GSE33513
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of TCF7 [GeneID=6932] deficient early thymic progenitors versus the TCF7 [GeneID=6932] sufficient ones.

description_full:
  Although transcriptional programs associated with T-cell specification and commitment have been described, the functional hierarchy and the roles of key regulators in structuring/ orchestrating these programs remain unclear. Activation of Notch signaling in uncommitted precursors by the thymic stroma initiates the T-cell differentiation program. One regulator first induced in these precursors is the DNA binding protein Tcf-1, a T-cell specific mediator of Wnt signaling. Yet the specific contribution of Tcf-1 to early T-cell development and the signals inducing it in these cells remain unclear. Here we assign functional significance to Tcf-1 as a gatekeeper of T-cell fate. We show that Tcf-1 is directly activated by Notch signals. Tcf-1 is required at the earliest phase of Tcell determination for progression beyond the early thymic progenitor (ETP) stage. The global expression profile of Tcf-1 deficient progenitors indicates that basic processes of DNA metabolism are downregulated in its absence and the blocked T-cell progenitors become abortive and die by apoptosis. Our data thus add an important functional relationship to the roadmap of T-cell development. We used microarrays to detail the global programme of gene expression of mouse ETP thymocyte after Ikaros inactivation with dominant negative of Ik at different stage.


systematic_name: M5107
exact_source: GSE33513_2166_200_DN
source_species_code: MM
GEO_id: GSE33513
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of TCF7 [GeneID=6932] deficient early thymic progenitors versus the TCF7 [GeneID=6932] sufficient ones.

description_full:
  Although transcriptional programs associated with T-cell specification and commitment have been described, the functional hierarchy and the roles of key regulators in structuring/ orchestrating these programs remain unclear. Activation of Notch signaling in uncommitted precursors by the thymic stroma initiates the T-cell differentiation program. One regulator first induced in these precursors is the DNA binding protein Tcf-1, a T-cell specific mediator of Wnt signaling. Yet the specific contribution of Tcf-1 to early T-cell development and the signals inducing it in these cells remain unclear. Here we assign functional significance to Tcf-1 as a gatekeeper of T-cell fate. We show that Tcf-1 is directly activated by Notch signals. Tcf-1 is required at the earliest phase of Tcell determination for progression beyond the early thymic progenitor (ETP) stage. The global expression profile of Tcf-1 deficient progenitors indicates that basic processes of DNA metabolism are downregulated in its absence and the blocked T-cell progenitors become abortive and die by apoptosis. Our data thus add an important functional relationship to the roadmap of T-cell development. We used microarrays to detail the global programme of gene expression of mouse ETP thymocyte after Ikaros inactivation with dominant negative of Ik at different stage.


description_brief: Genes up-regulated in comparison of CD4 [GeneID=920] dendritic cells (DC) versus CD8 DCs.
systematic_name: M5108
exact_source: GSE339_1505_200_UP
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The functional relationships and properties of different sub-types of dendritic cells (DC) remain largely undefined. We used a global gene profiling approach to determine gene expression patterns among murine splenic CD11c high DC subsets in an effort to better characterise these cells.


systematic_name: M5114
exact_source: GSE339_1506_200_UP
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4 [GeneID=920] dendritic cells (DC) versus CD4- [GeneID=920] CD8- DCs.

description_full:
  The functional relationships and properties of different sub-types of dendritic cells (DC) remain largely undefined. We used a global gene profiling approach to determine gene expression patterns among murine splenic CD11c high DC subsets in an effort to better characterise these cells.


systematic_name: M5116
exact_source: GSE339_1506_200_DN
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4 [GeneID=920] dendritic cells (DC) versus CD4- [GeneID=920] CD8- DCs.

description_full:
[cell repeats an earlier one in this file: 287 characters]


systematic_name: M5129
exact_source: GSE339_1511_200_UP
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of ex vivo CD4 [GeneID=920] dendritic cells (DC) versus cultured CD4 [GeneID=920] DCs.

description_full:
[cell repeats an earlier one in this file: 287 characters]


systematic_name: M5130
exact_source: GSE339_1511_200_DN
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of ex vivo CD4 [GeneID=920] dendritic cells (DC) versus cultured CD4 [GeneID=920] DCs.

description_full:
[cell repeats an earlier one in this file: 287 characters]


systematic_name: M5134
exact_source: GSE339_1513_200_UP
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of ex vivo CD4- [GeneID=920] CD8- dendritic cells (DC) versus cultured CD4- [GeneID=920] CD8- DCs.

description_full:
[cell repeats an earlier one in this file: 287 characters]


systematic_name: M5135
exact_source: GSE339_1513_200_DN
source_species_code: MM
GEO_id: GSE339
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of ex vivo CD4- [GeneID=920] CD8- dendritic cells (DC) versus cultured CD4- [GeneID=920] CD8- DCs.

description_full:
[cell repeats an earlier one in this file: 287 characters]


systematic_name: M5136
exact_source: GSE34205_2334_200_UP
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from infanct with acute RSV infection.

description_full:
  To study the transcriptional profile of patients with acute RSV or Influenza infection,children of median age 2.4 months (range 1.5-8.6) hospitalized with acute RSV and influenza virus infection were offered study enrollment after microbiologic confirmation of the diagnosis. Blood samples were collected from them within 42-72 hours of hospitalization. We excluded children with suspected or proven polymicrobial infections, with underlying chronic medical conditions (i.e congenital heart disease, renal insufficiency), with immunodeficiency, or those who received systemic steroids or other immunomodulatory therapies. The RSV cohort consisted of 51 patients with median age of 2 months (range 1.5-3.9) and the influenza cohort had 28 patients with median age of 5.5 months (range 1.4-21). Control samples were obtained from healthy children undergoing elective surgical procedures or at outpatient clinic visits. To exclude viral co-infections we performed nasopharyngeal viral cultures of all subjects. We recruited 10 control patients for the RSV cohort with median age of 6.7 months (range 5-10), and 12 control patients for the influenza cohort with median age of18.5 months (range 10.5-26).


systematic_name: M5137
exact_source: GSE34205_2334_200_DN
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from infanct with acute RSV infection.

description_full:
  To study the transcriptional profile of patients with acute RSV or Influenza infection,children of median age 2.4 months (range 1.5-8.6) hospitalized with acute RSV and influenza virus infection were offered study enrollment after microbiologic confirmation of the diagnosis. Blood samples were collected from them within 42-72 hours of hospitalization. We excluded children with suspected or proven polymicrobial infections, with underlying chronic medical conditions (i.e congenital heart disease, renal insufficiency), with immunodeficiency, or those who received systemic steroids or other immunomodulatory therapies. The RSV cohort consisted of 51 patients with median age of 2 months (range 1.5-3.9) and the influenza cohort had 28 patients with median age of 5.5 months (range 1.4-21). Control samples were obtained from healthy children undergoing elective surgical procedures or at outpatient clinic visits. To exclude viral co-infections we performed nasopharyngeal viral cultures of all subjects. We recruited 10 control patients for the RSV cohort with median age of 6.7 months (range 5-10), and 12 control patients for the influenza cohort with median age of18.5 months (range 10.5-26).


systematic_name: M5138
exact_source: GSE34205_2335_200_UP
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from infanct with acute influenza infection.

description_full:
  To study the transcriptional profile of patients with acute RSV or Influenza infection,children of median age 2.4 months (range 1.5-8.6) hospitalized with acute RSV and influenza virus infection were offered study enrollment after microbiologic confirmation of the diagnosis. Blood samples were collected from them within 42-72 hours of hospitalization. We excluded children with suspected or proven polymicrobial infections, with underlying chronic medical conditions (i.e congenital heart disease, renal insufficiency), with immunodeficiency, or those who received systemic steroids or other immunomodulatory therapies. The RSV cohort consisted of 51 patients with median age of 2 months (range 1.5-3.9) and the influenza cohort had 28 patients with median age of 5.5 months (range 1.4-21). Control samples were obtained from healthy children undergoing elective surgical procedures or at outpatient clinic visits. To exclude viral co-infections we performed nasopharyngeal viral cultures of all subjects. We recruited 10 control patients for the RSV cohort with median age of 6.7 months (range 5-10), and 12 control patients for the influenza cohort with median age of18.5 months (range 10.5-26).


systematic_name: M5139
exact_source: GSE34205_2335_200_DN
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from infanct with acute influenza infection.

description_full:
[cell repeats an earlier one in this file: 1199 characters]


systematic_name: M5141
exact_source: GSE34205_2336_200_UP
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from infancts with acute RSV infection versus PBMCs from infants with acute influenza infection.

description_full:
[cell repeats an earlier one in this file: 1199 characters]


systematic_name: M5142
exact_source: GSE34205_2336_200_DN
source_species_code: HS
GEO_id: GSE34205
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from infancts with acute RSV infection versus PBMCs from infants with acute influenza infection.

description_full:
[cell repeats an earlier one in this file: 1199 characters]


description_brief: Genes up-regulated in untreated dendritic cells (DC) versus DCs exposed to parasite L. donovani.
systematic_name: M5143
exact_source: GSE360_1001_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Monocyte-derived dendritic cells (DC) and macrophages (MΦ) generated in vitro from the same individual blood donors were exposed to five different pathogens, and gene expression profiles were assessed by microarray analysis. Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, L. donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger.


systematic_name: M5147
exact_source: GSE360_1003_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in untreated dendritic cells (DC) versus DCs exposed to parasite Toxoplasma gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5148
exact_source: GSE360_1003_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in untreated dendritic cells (DC) versus DCs exposed to parasite Toxoplasma gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5150
exact_source: GSE360_1004_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) versus DCs exposed to B. malayi (50 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5151
exact_source: GSE360_1004_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) versus DCs exposed to B. malayi (50 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5152
exact_source: GSE360_1005_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) versus DCs exposed to B. malayi (5 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5153
exact_source: GSE360_1005_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) versus DCs exposed to B. malayi (5 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5165
exact_source: GSE360_1010_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages versus macrophages exposed to B. malayi (50 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5167
exact_source: GSE360_1010_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages versus macrophages exposed to B. malayi (50 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5168
exact_source: GSE360_1011_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages versus macrophages exposed to B. malayi (5 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5169
exact_source: GSE360_1011_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages versus macrophages exposed to B. malayi (5 worms/well).

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5174
exact_source: GSE360_1014_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus macrophages exposed to L. donovani.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5176
exact_source: GSE360_1014_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus macrophages exposed to L. donovani.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5181
exact_source: GSE360_1015_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells exposed to L. major versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5182
exact_source: GSE360_1015_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells exposed to L. major versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5183
exact_source: GSE360_1016_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5184
exact_source: GSE360_1016_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5185
exact_source: GSE360_1017_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to 50 worm/well B. malayi versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5186
exact_source: GSE360_1017_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to 50 worm/well B. malayi versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5187
exact_source: GSE360_1018_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to 5 worm/well B. malayi versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5188
exact_source: GSE360_1018_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to 5 worm/well B. malayi versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5189
exact_source: GSE360_1019_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to M. tuberculosis versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5191
exact_source: GSE360_1019_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to M. tuberculosis versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5192
exact_source: GSE360_1020_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5194
exact_source: GSE360_1020_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5195
exact_source: GSE360_1021_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5196
exact_source: GSE360_1021_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5197
exact_source: GSE360_1022_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to 50 worm/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5201
exact_source: GSE360_1022_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to 50 worm/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5203
exact_source: GSE360_1023_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to 5 worm/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5204
exact_source: GSE360_1023_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to 5 worm/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5205
exact_source: GSE360_1024_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5206
exact_source: GSE360_1024_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. donovani versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5207
exact_source: GSE360_1025_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5208
exact_source: GSE360_1025_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5209
exact_source: GSE360_1026_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5210
exact_source: GSE360_1026_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5211
exact_source: GSE360_1027_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5212
exact_source: GSE360_1027_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5213
exact_source: GSE360_1028_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5214
exact_source: GSE360_1028_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to L. major versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5215
exact_source: GSE360_1029_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5216
exact_source: GSE360_1029_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5217
exact_source: GSE360_1030_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5219
exact_source: GSE360_1030_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5220
exact_source: GSE360_1031_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5221
exact_source: GSE360_1031_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to T. gondii versus DCs exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5222
exact_source: GSE360_1032_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to 50 worms/well B. malayi versus those exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5225
exact_source: GSE360_1032_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to 50 worms/well B. malayi versus those exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5227
exact_source: GSE360_1033_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to 50 worms/well B. malayi versus DC exposed to M. tuberculosis

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5228
exact_source: GSE360_1033_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to 50 worms/well B. malayi versus DC exposed to M. tuberculosis

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5229
exact_source: GSE360_1034_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) exposed to 5 worms/well B. malayi versus DC exposed to M. tuberculosis

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5230
exact_source: GSE360_1034_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) exposed to 5 worms/well B. malayi versus DC exposed to M. tuberculosis

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5231
exact_source: GSE360_1035_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5232
exact_source: GSE360_1035_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to L. major.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5233
exact_source: GSE360_1036_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5234
exact_source: GSE360_1036_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5235
exact_source: GSE360_1037_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5237
exact_source: GSE360_1037_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5239
exact_source: GSE360_1038_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5240
exact_source: GSE360_1038_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5241
exact_source: GSE360_1039_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5242
exact_source: GSE360_1039_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. donovani versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5243
exact_source: GSE360_1040_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5246
exact_source: GSE360_1040_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to T. gondii.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5247
exact_source: GSE360_1041_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5249
exact_source: GSE360_1041_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5250
exact_source: GSE360_1042_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5251
exact_source: GSE360_1042_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5252
exact_source: GSE360_1043_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5253
exact_source: GSE360_1043_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to L. major versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5254
exact_source: GSE360_1044_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to T. gondii versus  macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5255
exact_source: GSE360_1044_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to T. gondii versus  macrophages exposed to 50 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5256
exact_source: GSE360_1045_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to T. gondii versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5257
exact_source: GSE360_1045_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to T. gondii versus macrophages exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5258
exact_source: GSE360_1046_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to T. gondii versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5259
exact_source: GSE360_1046_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to T. gondii versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5261
exact_source: GSE360_1047_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to 50 worms/well B. malayi versus those exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5262
exact_source: GSE360_1047_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to 50 worms/well B. malayi versus those exposed to 5 worms/well B. malayi.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5263
exact_source: GSE360_1048_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to 50 worms/well B. malayi versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5264
exact_source: GSE360_1048_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to 50 worms/well B. malayi versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5266
exact_source: GSE360_1049_200_UP
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages exposed to 5 worms/well B. malayi versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5268
exact_source: GSE360_1049_200_DN
source_species_code: HS
GEO_id: GSE360
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages exposed to 5 worms/well B. malayi versus macrophages exposed to M. tuberculosis.

description_full:
[cell repeats an earlier one in this file: 538 characters]


systematic_name: M5270
exact_source: GSE36392_2066_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus eosinophils treated with IL25 [GeneID=64806].

description_full:
  Many symptoms associated with allergic asthma result from the sequelae of type 2 inflammation. Interleukin (IL)-25 promotes type 2 inflammatory responses, and T2M cells represent an IL-4 and IL-13 producing granulocytic IL-25 responsive population. We used microarrays to characterize the gene expression profile of T2M cells, and compared T2M cells to other inflammatory subsets (eosinophils, neutrophils, and macrophages) in the lungs of mice with IL-25-induced pulmonary inflammation.


systematic_name: M5271
exact_source: GSE36392_2066_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus eosinophils treated with IL25 [GeneID=64806].

description_full:
  Many symptoms associated with allergic asthma result from the sequelae of type 2 inflammation. Interleukin (IL)-25 promotes type 2 inflammatory responses, and T2M cells represent an IL-4 and IL-13 producing granulocytic IL-25 responsive population. We used microarrays to characterize the gene expression profile of T2M cells, and compared T2M cells to other inflammatory subsets (eosinophils, neutrophils, and macrophages) in the lungs of mice with IL-25-induced pulmonary inflammation.


systematic_name: M5273
exact_source: GSE36392_2067_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus macrophages treated with IL25 [GeneID=64806].

description_full:
  Many symptoms associated with allergic asthma result from the sequelae of type 2 inflammation. Interleukin (IL)-25 promotes type 2 inflammatory responses, and T2M cells represent an IL-4 and IL-13 producing granulocytic IL-25 responsive population. We used microarrays to characterize the gene expression profile of T2M cells, and compared T2M cells to other inflammatory subsets (eosinophils, neutrophils, and macrophages) in the lungs of mice with IL-25-induced pulmonary inflammation.


systematic_name: M5274
exact_source: GSE36392_2067_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus macrophages treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5276
exact_source: GSE36392_2068_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5277
exact_source: GSE36392_2068_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of type 2 myeloid (T2M) cells treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5280
exact_source: GSE36392_2069_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of eosinophils treated with IL25 [GeneID=64806] versus macrophages treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5281
exact_source: GSE36392_2069_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of eosinophils treated with IL25 [GeneID=64806] versus macrophages treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5282
exact_source: GSE36392_2070_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of eosinophils treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5284
exact_source: GSE36392_2070_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of eosinophils treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5285
exact_source: GSE36392_2071_200_UP
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5286
exact_source: GSE36392_2071_200_DN
source_species_code: MM
GEO_id: GSE36392
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages treated with IL25 [GeneID=64806] versus neutrophils treated with IL25 [GeneID=64806].

description_full:
[cell repeats an earlier one in this file: 487 characters]


systematic_name: M5287
exact_source: GSE36476_1728_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 16 h.

description_full:
  With increasing age, the ability of the immune system to protect against recurring infections or to control chronic infections erodes. The objective of the current study was to identify gene expression signatures in elderly CD4 T cell responses


systematic_name: M5288
exact_source: GSE36476_1728_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 16 h.

description_full:
  With increasing age, the ability of the immune system to protect against recurring infections or to control chronic infections erodes. The objective of the current study was to identify gene expression signatures in elderly CD4 T cell responses


systematic_name: M5289
exact_source: GSE36476_1729_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 40 h.

description_full:
  With increasing age, the ability of the immune system to protect against recurring infections or to control chronic infections erodes. The objective of the current study was to identify gene expression signatures in elderly CD4 T cell responses


systematic_name: M5292
exact_source: GSE36476_1729_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 40 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5293
exact_source: GSE36476_1730_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5294
exact_source: GSE36476_1730_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from young donors versus those treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5295
exact_source: GSE36476_1731_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 16 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5296
exact_source: GSE36476_1731_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 16 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5299
exact_source: GSE36476_1732_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 40 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5300
exact_source: GSE36476_1732_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 40 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5302
exact_source: GSE36476_1733_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5303
exact_source: GSE36476_1733_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] memory T cells from old donors versus those treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5306
exact_source: GSE36476_1734_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated memory CD4 [GeneID=920] T cells from young donors versus those from old donors.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5307
exact_source: GSE36476_1734_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated memory CD4 [GeneID=920] T cells from young donors versus those from old donors.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5313
exact_source: GSE36476_1735_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 16 h versus those from old donors treated with TSST at 16 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5317
exact_source: GSE36476_1735_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 16 h versus those from old donors treated with TSST at 16 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5318
exact_source: GSE36476_1736_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 40 h versus those from old donors treated with TSST at 40 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5322
exact_source: GSE36476_1736_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 40 h versus those from old donors treated with TSST at 40 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5323
exact_source: GSE36476_1737_200_UP
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 72 h versus those from old donors treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5324
exact_source: GSE36476_1737_200_DN
source_species_code: HS
GEO_id: GSE36476
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of memory CD4 [GeneID=920] T cells from young donors treated with TSST at 72 h versus those from old donors treated with TSST at 72 h.

description_full:
[cell repeats an earlier one in this file: 244 characters]


systematic_name: M5326
exact_source: GSE37416_2050_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 0 h.

description_full:
  We demonstrated recently that both constitutive and FAS-triggered apoptosis of human neutrophils are profoundly impaired by Francisella tularensis, but how this is achieved is largely unknown. To test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, we used human oligonucleotide microarrays to identify differentially regulated genes in cells infected with F. tularensis strain LVS compared with uninfected controls. In order to examine the effect of F. tularensis on the neutrophil transcriptome, we performed microarray expression analysis on human neutrophils treated with F. tularensis subsp. holarctica live vaccine strain (LVS).


systematic_name: M5327
exact_source: GSE37416_2050_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 0 h.

description_full:
  We demonstrated recently that both constitutive and FAS-triggered apoptosis of human neutrophils are profoundly impaired by Francisella tularensis, but how this is achieved is largely unknown. To test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, we used human oligonucleotide microarrays to identify differentially regulated genes in cells infected with F. tularensis strain LVS compared with uninfected controls. In order to examine the effect of F. tularensis on the neutrophil transcriptome, we performed microarray expression analysis on human neutrophils treated with F. tularensis subsp. holarctica live vaccine strain (LVS).


systematic_name: M5328
exact_source: GSE37416_2051_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 3 h versus PMN treated with F. tularensis vaccine at 3 h.

description_full:
  We demonstrated recently that both constitutive and FAS-triggered apoptosis of human neutrophils are profoundly impaired by Francisella tularensis, but how this is achieved is largely unknown. To test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, we used human oligonucleotide microarrays to identify differentially regulated genes in cells infected with F. tularensis strain LVS compared with uninfected controls. In order to examine the effect of F. tularensis on the neutrophil transcriptome, we performed microarray expression analysis on human neutrophils treated with F. tularensis subsp. holarctica live vaccine strain (LVS).


systematic_name: M5330
exact_source: GSE37416_2051_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 3 h versus PMN treated with F. tularensis vaccine at 3 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5332
exact_source: GSE37416_2052_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 6 h versus PMN treated with F. tularensis vaccine at 6 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5333
exact_source: GSE37416_2052_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 6 h versus PMN treated with F. tularensis vaccine at 6 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5334
exact_source: GSE37416_2053_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 12 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5335
exact_source: GSE37416_2053_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 12 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5337
exact_source: GSE37416_2054_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 24 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5338
exact_source: GSE37416_2054_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 24 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5339
exact_source: GSE37416_2055_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 48 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5340
exact_source: GSE37416_2055_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 48 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5341
exact_source: GSE37416_2056_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 3 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5342
exact_source: GSE37416_2056_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 3 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5344
exact_source: GSE37416_2057_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 6 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5346
exact_source: GSE37416_2057_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 6 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5347
exact_source: GSE37416_2058_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 12 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5348
exact_source: GSE37416_2058_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 12 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5349
exact_source: GSE37416_2059_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5350
exact_source: GSE37416_2059_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5351
exact_source: GSE37416_2060_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5353
exact_source: GSE37416_2060_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 0 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5357
exact_source: GSE37416_2064_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5358
exact_source: GSE37416_2064_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 24 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5359
exact_source: GSE37416_2065_200_UP
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5361
exact_source: GSE37416_2065_200_DN
source_species_code: HS
GEO_id: GSE37416
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control polymorphonuclear leukocytes (PMN) at 12 h versus PMN treated with F. tularensis vaccine at 48 h.

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5363
exact_source: GSE3982_1761_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated eosinophils versus eosinophils treated with PMA [PubChem=4792] at 2 h.

description_full:
  In the present study we used Affymetrix oligonucleotide microarrays to produce gene transcription profiles for the major leukocyte types in humans. This comprehensive dataset enabled us to not only establish which genes were expressed in each leukocyte type, but also which genes were expressed in each subset after activation. The used of a comprehensive dataset of gene profiles from all the major human leukocyte subsets enabled a novel and powerful means for identification of genes associated with single leukocyte subsets, or different immune paradigms.


systematic_name: M5364
exact_source: GSE3982_1761_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated eosinophils versus eosinophils treated with PMA [PubChem=4792] at 2 h.

description_full:
  In the present study we used Affymetrix oligonucleotide microarrays to produce gene transcription profiles for the major leukocyte types in humans. This comprehensive dataset enabled us to not only establish which genes were expressed in each leukocyte type, but also which genes were expressed in each subset after activation. The used of a comprehensive dataset of gene profiles from all the major human leukocyte subsets enabled a novel and powerful means for identification of genes associated with single leukocyte subsets, or different immune paradigms.


systematic_name: M5366
exact_source: GSE3982_1762_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated mast cells versus mast cells treated with IgE at 2 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5367
exact_source: GSE3982_1763_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages versus macrophages treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5368
exact_source: GSE3982_1763_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages versus macrophages treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5371
exact_source: GSE3982_1764_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated neutrophils versus neutrophils treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5373
exact_source: GSE3982_1764_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated neutrophils versus neutrophils treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5375
exact_source: GSE3982_1765_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated dendritic cells (DC) versus DCs treated with LPS (TLR4 agonist) at 48 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5377
exact_source: GSE3982_1765_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated dendritic cells (DC) versus DCs treated with LPS (TLR4 agonist) at 48 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5387
exact_source: GSE3982_1769_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) stimulatd with LPS (TLR4 agonist) at 48 h versus macrophages stimulated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5390
exact_source: GSE3982_1769_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) stimulatd with LPS (TLR4 agonist) at 48 h versus macrophages stimulated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5391
exact_source: GSE3982_1770_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) stimulated with LPS (TLR4 agonist) at 48 h versus neutrophils stimulated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5393
exact_source: GSE3982_1770_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) stimulated with LPS (TLR4 agonist) at 48 h versus neutrophils stimulated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5394
exact_source: GSE3982_1771_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of macrophages stimulated with LPS (TLR4 agonist) at 4 h versus neutrophils stimulated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5396
exact_source: GSE3982_1771_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of macrophages stimulated with LPS (TLR4 agonist) at 4 h versus neutrophils stimulated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5474
exact_source: GSE3982_1797_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) versus effector memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5475
exact_source: GSE3982_1797_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) versus effector memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5476
exact_source: GSE3982_1798_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of dendritic cells (DC) versus central memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5477
exact_source: GSE3982_1798_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of dendritic cells (DC) versus central memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5569
exact_source: GSE3982_1828_200_UP
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of effective memory CD4 [GeneID=920] T cells versus central memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5571
exact_source: GSE3982_1828_200_DN
source_species_code: HS
GEO_id: GSE3982
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of effective memory CD4 [GeneID=920] T cells versus central memory CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 559 characters]


systematic_name: M5599
exact_source: GSE39820_1555_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with IL1B [GeneID=3553] and IL6 [GeneID=3569].

description_full:
  TGF-beta3 produced by developing Th17 cells induces highly pathogenic T cells that are functionally and molecularly distinct from TGF-beta1-induced Th17 cells. The microarray data represent a distinct molecular signature for pathogenic versus non-pathogenic Th17 cells.


systematic_name: M5600
exact_source: GSE39820_1555_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with IL1B [GeneID=3553] and IL6 [GeneID=3569].

description_full:
  TGF-beta3 produced by developing Th17 cells induces highly pathogenic T cells that are functionally and molecularly distinct from TGF-beta1-induced Th17 cells. The microarray data represent a distinct molecular signature for pathogenic versus non-pathogenic Th17 cells.


systematic_name: M5602
exact_source: GSE39820_1556_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated witl IL1B [GeneID=3553],  IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
  TGF-beta3 produced by developing Th17 cells induces highly pathogenic T cells that are functionally and molecularly distinct from TGF-beta1-induced Th17 cells. The microarray data represent a distinct molecular signature for pathogenic versus non-pathogenic Th17 cells.


systematic_name: M5603
exact_source: GSE39820_1556_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with IL1B [GeneID=3553],  IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5604
exact_source: GSE39820_1557_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB1 [GeneID=7040] and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5606
exact_source: GSE39820_1557_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB1 [GeneID=7040] and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5607
exact_source: GSE39820_1558_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB1 [GeneID=7040], IL6 [GeneID=3569]  and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5609
exact_source: GSE39820_1558_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB1 [GeneID=7040], IL6 [GeneID=3569]  and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5610
exact_source: GSE39820_1559_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB3 [GeneID=7043] IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5612
exact_source: GSE39820_1559_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB3 [GeneID=7043] IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5613
exact_source: GSE39820_1560_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB3 [GeneID=7043], IL6 [GeneID=3569] and IL32A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5614
exact_source: GSE39820_1560_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells versus those treated with TGFB3 [GeneID=7043], IL6 [GeneID=3569] and IL32A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5615
exact_source: GSE39820_1561_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated CD4 [GeneID=920] T cells treated with IL1B [GeneID=3553] and IL6 [GeneID=3569] versus those treated with IL1B [GeneID=3553], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5616
exact_source: GSE39820_1561_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated CD4 [GeneID=920] T cells treated with IL1B [GeneID=3553] and IL6 [GeneID=3569] versus those treated with IL1B [GeneID=3553], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5617
exact_source: GSE39820_1562_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] and IL6 [GeneID=3569] versus those treated with TGFB1 [GeneID=7040], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5619
exact_source: GSE39820_1562_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] and IL6 [GeneID=3569] versus those treated with TGFB1 [GeneID=7040], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5620
exact_source: GSE39820_1563_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB3 [GeneID=7043] and IL6 [GeneID=3569] versus those treated with TGF3B [GeneID=7043], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5621
exact_source: GSE39820_1563_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB3 [GeneID=7043] and IL6 [GeneID=3569] versus those treated with TGF3B [GeneID=7043], IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5623
exact_source: GSE39820_1564_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] versus those treated with TGFB3 [GeneID=7043] and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5626
exact_source: GSE39820_1564_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] versus those treated with TGFB3 [GeneID=7043] and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5627
exact_source: GSE39820_1565_200_UP
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] versus those treated with TGFB3 [GeneID=7043] treated with IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5629
exact_source: GSE39820_1565_200_DN
source_species_code: MM
GEO_id: GSE39820
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of CD4 [GeneID=920] T cells treated with TGFB1 [GeneID=7040] versus those treated with TGFB3 [GeneID=7043] treated with IL6 [GeneID=3569] and IL23A [GeneID=51561].

description_full:
[cell repeats an earlier one in this file: 269 characters]


systematic_name: M5630
exact_source: GSE5463_2129_200_UP
source_species_code: MM
GEO_id: GSE5463
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control thymocytes versus thymocytes treated with dexamethasone [PubChem=5743].

description_full:
  Glucocorticoids play a role in regulation of T lymphocytes homeostasis and development. In particular, glucocorticoid treatment induces massive apoptosis of CD4+CD8+ double positive (DP) thymocytes. This effect is due to many mechanisms, mainly driven by modulation of gene transcription. To find out which genes are modulated, we analyzed DP thymocytes treated for 3 hours with dexamethasone or medium alone, by global gene expression profiling using the Affymetrix technology (MGU74Av2 GeneChip). The data were analyzed with MAS 5.0 imposing a cut off of 1.7 fold in up regulation and 1.35 fold in down regulation. To further filter results we also used the statistical software, SAM (d 0.88 see figure 1s in supplementary data of the above cited manuscript). Results indicate modulation of 156 genes, also confirmed by either RNAse protection assay or Real Time PCR. For data mining we also used Go Miner to explore the Gene Ontology data bank (see tables 1-3 of the above cited manuscript). The overall results demonstrated that dexamethasone caused the down-regulation of genes promoting survival of DP thymocytes (e.g. Notch1, Socs1 and Id3) or the modulation of genes activating cell death through the ceramide pathway (Ugcg, Sgpp1, Degs1 and Gpr65) or through the mithocondrial machinery. Among the latter, there are Bcl-2 family members (Bim, Bfl-1, Bcl-xL and Bcl-xbeta), genes involved in the control of redox status (thioredoxin reductase, TXNIP and idh2) and genes belonging to Tis11 family which are involved in mRNA stability. Our study suggests that dexamethasone treatment of DP thymocytes modulates several genes belonging to apoptosis-related systems that can contribute to their apoptosis. 


systematic_name: M5632
exact_source: GSE5463_2129_200_DN
source_species_code: MM
GEO_id: GSE5463
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control thymocytes versus thymocytes treated with dexamethasone [PubChem=5743].

description_full:
  Glucocorticoids play a role in regulation of T lymphocytes homeostasis and development. In particular, glucocorticoid treatment induces massive apoptosis of CD4+CD8+ double positive (DP) thymocytes. This effect is due to many mechanisms, mainly driven by modulation of gene transcription. To find out which genes are modulated, we analyzed DP thymocytes treated for 3 hours with dexamethasone or medium alone, by global gene expression profiling using the Affymetrix technology (MGU74Av2 GeneChip). The data were analyzed with MAS 5.0 imposing a cut off of 1.7 fold in up regulation and 1.35 fold in down regulation. To further filter results we also used the statistical software, SAM (d 0.88 see figure 1s in supplementary data of the above cited manuscript). Results indicate modulation of 156 genes, also confirmed by either RNAse protection assay or Real Time PCR. For data mining we also used Go Miner to explore the Gene Ontology data bank (see tables 1-3 of the above cited manuscript). The overall results demonstrated that dexamethasone caused the down-regulation of genes promoting survival of DP thymocytes (e.g. Notch1, Socs1 and Id3) or the modulation of genes activating cell death through the ceramide pathway (Ugcg, Sgpp1, Degs1 and Gpr65) or through the mithocondrial machinery. Among the latter, there are Bcl-2 family members (Bim, Bfl-1, Bcl-xL and Bcl-xbeta), genes involved in the control of redox status (thioredoxin reductase, TXNIP and idh2) and genes belonging to Tis11 family which are involved in mRNA stability. Our study suggests that dexamethasone treatment of DP thymocytes modulates several genes belonging to apoptosis-related systems that can contribute to their apoptosis. 


systematic_name: M5637
exact_source: GSE5960_1852_200_UP
source_species_code: MM
GEO_id: GSE5960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of anergy induced CD4 [GeneID=920] T cells versus conventional CD4 [GeneID=920] T cells.

description_full:
  compare gene expression profiles between normal and anergic T cells and identify upregulated genes in anergic T cells


systematic_name: M5638
exact_source: GSE5960_1852_200_DN
source_species_code: MM
GEO_id: GSE5960
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of anergy induced CD4 [GeneID=920] T cells versus conventional CD4 [GeneID=920] T cells.

description_full:
  compare gene expression profiles between normal and anergic T cells and identify upregulated genes in anergic T cells


systematic_name: M5639
exact_source: GSE6269_1514_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute influenza infection.

description_full:
  Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.


systematic_name: M5640
exact_source: GSE6269_1514_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute influenza infection.

description_full:
  Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.


systematic_name: M5641
exact_source: GSE6269_1515_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute E. coli infection.

description_full:
  Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.


systematic_name: M5642
exact_source: GSE6269_1515_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute E. coli infection.

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


systematic_name: M5643
exact_source: GSE6269_1516_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5644
exact_source: GSE6269_1516_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5648
exact_source: GSE6269_1517_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5649
exact_source: GSE6269_1517_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5653
exact_source: GSE6269_1518_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute E. coli infection.

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


systematic_name: M5654
exact_source: GSE6269_1518_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute E. coli infection.

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


systematic_name: M5655
exact_source: GSE6269_1519_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5656
exact_source: GSE6269_1519_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5657
exact_source: GSE6269_1520_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5658
exact_source: GSE6269_1520_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute influenza infection versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5659
exact_source: GSE6269_1521_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute E. coli infection versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5660
exact_source: GSE6269_1521_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute E. coli infection versus PBMC from patients with acute S. aureus infection.

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


systematic_name: M5661
exact_source: GSE6269_1522_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute E. coli infection versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5662
exact_source: GSE6269_1522_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute E. coli infection versus PBMC from patients with acute S. pneumoniae infection.

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


systematic_name: M5663
exact_source: GSE6269_1523_200_UP
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute infection: S. aureus versus S. pneumoniae.

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


systematic_name: M5664
exact_source: GSE6269_1523_200_DN
source_species_code: HS
GEO_id: GSE6269
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with acute infection: S. aureus versus S. pneumoniae.

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


systematic_name: M5665
exact_source: GSE6566_1724_200_UP
source_species_code: HS
GEO_id: GSE6566
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] cells stimulated with strong dendritic cells (DC) versus CD4 [GeneID=920] T cells stimulated with weak DCs.

description_full:
  The strength of T cell stimulation determines IL-7 responsiveness, recall potential and lineage commitment of primed human CD4+IL-7Rhi T cells. We analyzed how the strength of antigenic stimulation - as determined by dendritic cell (DC) number, DC maturation state and antigen concentration - controls in human CD4+ T cells IL-7R-alpha expression and responsiveness to IL-7, IL-15 and antigen. We found that T cells primed by different strengths of stimulation expressed IL-7R-alpha in different proportions and preferentially on cells that maintained expression of the central memory marker CCR7. However, while CCR7+IL-7Rhi cells generated at high strength of stimulation proliferated vigorously in response to IL-7 or IL-15, CCR7+IL-7Rhi cells generated at low strength of stimulation responded poorly. High cytokine responsiveness was associated with reduced PTEN expression and enhanced s6-kinase activation, consistent with efficient receptor coupling to downstream signalling pathways. Interestingly, while intermediate-stimulated CCR7+IL-7Rhi cells were non-polarized, self-renewed with IL-7 and expanded with antigen, high-stimulated cells generated Th1 effector cells with cytokines but showed impaired IL-2 production and survival with antigen. Gene expression analysis suggested that high-stimulated cells represented pre-Th1 cells with low recall potential and high metabolic state. Taken together these results demonstrate that IL-7 receptor expression and coupling are instructed in T cells by the strength of stimulation and suggest that memory subsets may derive from CCR7+IL-7Rhi precursors that received different strengths of stimulation.


systematic_name: M5666
exact_source: GSE6566_1724_200_DN
source_species_code: HS
GEO_id: GSE6566
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] cells stimulated with strong dendritic cells (DC) versus CD4 [GeneID=920] T cells stimulated with weak DCs.

description_full:
  The strength of T cell stimulation determines IL-7 responsiveness, recall potential and lineage commitment of primed human CD4+IL-7Rhi T cells. We analyzed how the strength of antigenic stimulation - as determined by dendritic cell (DC) number, DC maturation state and antigen concentration - controls in human CD4+ T cells IL-7R-alpha expression and responsiveness to IL-7, IL-15 and antigen. We found that T cells primed by different strengths of stimulation expressed IL-7R-alpha in different proportions and preferentially on cells that maintained expression of the central memory marker CCR7. However, while CCR7+IL-7Rhi cells generated at high strength of stimulation proliferated vigorously in response to IL-7 or IL-15, CCR7+IL-7Rhi cells generated at low strength of stimulation responded poorly. High cytokine responsiveness was associated with reduced PTEN expression and enhanced s6-kinase activation, consistent with efficient receptor coupling to downstream signalling pathways. Interestingly, while intermediate-stimulated CCR7+IL-7Rhi cells were non-polarized, self-renewed with IL-7 and expanded with antigen, high-stimulated cells generated Th1 effector cells with cytokines but showed impaired IL-2 production and survival with antigen. Gene expression analysis suggested that high-stimulated cells represented pre-Th1 cells with low recall potential and high metabolic state. Taken together these results demonstrate that IL-7 receptor expression and coupling are instructed in T cells by the strength of stimulation and suggest that memory subsets may derive from CCR7+IL-7Rhi precursors that received different strengths of stimulation.


systematic_name: M5668
exact_source: GSE7400_2048_200_UP
source_species_code: HS
GEO_id: GSE7400
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated peripheral blood mononuclear cells (PBMC) versus PBMCs treated with CSF3 [GeneID=1440].

description_full:
  Granulocyte-colony stimulating factor (G-CSF) is used to boost granulocyte counts in immunocompromised patients, but its effects on the immune system may be counter productive. We tested the hypothesis that G-CSF mobilized peripheral blood stem cell (PBSC) products are immunologically down regulated based on gene microarray analysis. Ten peripheral blood samples from normal donors for allogeneic PBSC transplantation were obtained before and after administration of G-CSF and tested on Affymetrix Human U133 Plus 2.0 GeneChip® microarrays. Significant changes in gene expression after G-CSF mobilization were reported by controlling the false discovery rate at 5%. Immune-related genes were isolated from the data set and categorized according to probe set annotations and a thorough, independent literature search. We found that G-CSF up-regulated inflammatory and neutrophil activation pathway gene expression; however, adaptive immune-related gene expression, such as antigen presentation, co-stimulation, T cell activation and cytolytic effector pathways, were generally down-regulated. Thus, despite significant increases in stem cells, lymphocytes and antigen presenting cells, G-CSF mobilized PBSC allografts exhibit a suppressive adaptive immune-related gene expression profile. Our data provides an explanation for the potentially immunosuppressive effects observed after G-CSF administration.


systematic_name: M5670
exact_source: GSE7400_2048_200_DN
source_species_code: HS
GEO_id: GSE7400
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated peripheral blood mononuclear cells (PBMC) versus PBMCs treated with CSF3 [GeneID=1440].

description_full:
  Granulocyte-colony stimulating factor (G-CSF) is used to boost granulocyte counts in immunocompromised patients, but its effects on the immune system may be counter productive. We tested the hypothesis that G-CSF mobilized peripheral blood stem cell (PBSC) products are immunologically down regulated based on gene microarray analysis. Ten peripheral blood samples from normal donors for allogeneic PBSC transplantation were obtained before and after administration of G-CSF and tested on Affymetrix Human U133 Plus 2.0 GeneChip® microarrays. Significant changes in gene expression after G-CSF mobilization were reported by controlling the false discovery rate at 5%. Immune-related genes were isolated from the data set and categorized according to probe set annotations and a thorough, independent literature search. We found that G-CSF up-regulated inflammatory and neutrophil activation pathway gene expression; however, adaptive immune-related gene expression, such as antigen presentation, co-stimulation, T cell activation and cytolytic effector pathways, were generally down-regulated. Thus, despite significant increases in stem cells, lymphocytes and antigen presenting cells, G-CSF mobilized PBSC allografts exhibit a suppressive adaptive immune-related gene expression profile. Our data provides an explanation for the potentially immunosuppressive effects observed after G-CSF administration.


description_brief: Genes up-regulated in comparison of TconvLN versus TregLN (see Fig. 1 in the paper for details).
systematic_name: M5673
exact_source: GSE7460_1327_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The transcription factor Foxp3 is usually considered the master regulator for the CD4+CD25+ "Treg" lineage, which plays a key role in controlling immune and autoimmune responses, and is characterized by a unique transcriptional signature. We have performed a meta-analysis of this signature in Treg cells in several conditions to delineate the elements that can be ascribed to T cell activation, TGFbeta signaling, or Foxp3 itself. We find that these influences synergize to activate many of the signature’s components. Foxp3 and TGFbeta signaling have interconnected relationships, as Foxp3 is induced by TGFbeta while enhancing TGFbeta’s positive feedback loop. Much of the Treg signature cannot be ascribed to Foxp3, as it contains gene clusters that are co-regulated, but cannot be transactivated, by Foxp3. This suggests that the Treg lineage is specified at a higher level of regulation, upstream of Foxp3, which does control some of the lineage’s essential immunoregulatory attributes.


systematic_name: M5676
exact_source: GSE7460_1328_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of TconvThy versus TregThy (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5679
exact_source: GSE7460_1329_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of ActCD8 versus ActCD8TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5680
exact_source: GSE7460_1330_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparsion of ActTreg versus ActTregTGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5682
exact_source: GSE7460_1330_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of ActTreg versus ActTregTGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5692
exact_source: GSE7460_1334_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparsion of ActTregTGF versus ActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5693
exact_source: GSE7460_1334_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of ActTregTGF versus ActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5695
exact_source: GSE7460_1335_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of ActCD4 versus ActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5696
exact_source: GSE7460_1336_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparsion of WTActCD4 versus WTActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5697
exact_source: GSE7460_1336_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of WTActCD4 versus WTActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5698
exact_source: GSE7460_1337_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparsion of sfActCD4 versus sfActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5699
exact_source: GSE7460_1337_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of sfActCD4 versus sfActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5703
exact_source: GSE7460_1339_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparsion of sfActCD4TGF versus ActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5705
exact_source: GSE7460_1339_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of sfActCD4TGF versus ActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5707
exact_source: GSE7460_1340_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparsion of sfActCD4 versus WTActCD4 (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5711
exact_source: GSE7460_1343_200_UP
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of ActCD4TGF versus WTActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


systematic_name: M5712
exact_source: GSE7460_1343_200_DN
source_species_code: HS
GEO_id: GSE7460
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of ActCD4TGF versus WTActCD4TGF (see Fig. 1 in the paper for details).

description_full:
[cell repeats an earlier one in this file: 992 characters]


description_brief: Genes up-regulated in comparison of NK cells versus total splenocytes.
systematic_name: M5720
exact_source: GSE7764_1056_200_UP
source_species_code: MM
GEO_id: GSE7764
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Murine NK cells were compared at rest and following 24 hours of IL-15 stimulation for their mRNA expression profiles on the Affymetrix MOE430_2 microarray platform. Additional comparators included resting bulk splenocytes.


systematic_name: M5723
exact_source: GSE7764_1057_200_UP
source_species_code: MM
GEO_id: GSE7764
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of NK cells treated with IL15 [GeneID=3567] versus untreated NK cells.

description_full:
  Murine NK cells were compared at rest and following 24 hours of IL-15 stimulation for their mRNA expression profiles on the Affymetrix MOE430_2 microarray platform. Additional comparators included resting bulk splenocytes.


systematic_name: M5724
exact_source: GSE7764_1057_200_DN
source_species_code: MM
GEO_id: GSE7764
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of NK cells treated with IL15 [GeneID=3567] versus untreated NK cells.

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


systematic_name: M5725
exact_source: GSE7764_1058_200_UP
source_species_code: MM
GEO_id: GSE7764
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of NK cells treated with IL15 [GeneID=3567] versus total splenocytes.

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


systematic_name: M5726
exact_source: GSE7764_1058_200_DN
source_species_code: MM
GEO_id: GSE7764
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of NK cells treated with IL15 [GeneID=3567] versus total splenocytes.

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


systematic_name: M5727
exact_source: GSE7852_1492_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of lymph node regulatory T cells versus lymph node conventional T cells.

description_full:
  Comparisons of global gene-expression profiles revealed a greater distinction between CD4+ Treg cells and CD4+ conventional (Tconv) T cells residing in abdominal (epidydimal) fat versus in more standard locations such as the spleen, thymus and LN.


systematic_name: M5729
exact_source: GSE7852_1492_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of lymph node regulatory T cells versus lymph node conventional T cells.

description_full:
  Comparisons of global gene-expression profiles revealed a greater distinction between CD4+ Treg cells and CD4+ conventional (Tconv) T cells residing in abdominal (epidydimal) fat versus in more standard locations such as the spleen, thymus and LN.


systematic_name: M5733
exact_source: GSE7852_1494_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of fat tissue regulatory T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5735
exact_source: GSE7852_1494_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of fat tissue regulatory T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5738
exact_source: GSE7852_1495_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of lymph node regulatory T cells versus thymus regulatory T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5739
exact_source: GSE7852_1496_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of lymph node regulatory T cells versus fat tissue regulatory T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5742
exact_source: GSE7852_1496_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of lymph node regulatory T cells versus fat tissue regulatory T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5744
exact_source: GSE7852_1497_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of thymus regulatory T cells versus fat tissue regulatory T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5745
exact_source: GSE7852_1498_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of lymph node conventional T cells versus thymus conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5746
exact_source: GSE7852_1498_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of lymph node conventional T cells versus thymus conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5747
exact_source: GSE7852_1499_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of lymph node conventional T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5748
exact_source: GSE7852_1499_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of lymph node conventional T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5749
exact_source: GSE7852_1500_200_UP
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of thymus conventional T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5750
exact_source: GSE7852_1500_200_DN
source_species_code: MM
GEO_id: GSE7852
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of thymus conventional T cells versus fat tissue conventional T cells.

description_full:
[cell repeats an earlier one in this file: 247 characters]


systematic_name: M5753
exact_source: GSE8384_1759_200_UP
source_species_code: MM
GEO_id: GSE8384
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of control RAW264.7 cells (macrophages) versus those infected with B. abortus.

description_full:
  Identification of host responses at the gene transcription level provides a molecular profile of the events that occur following infection. Brucella abortus is a facultative intracellular pathogen of macrophages that induces chronic infection in humans and domestic animals. Using microarray technology, the response of macrophages 4 hours following B. abortus infection was analyzed to identify early intracellular infection events that occur in macrophages. Of the more than 6,000 genes, we identified over 140 genes that were reproducibly differentially transcribed. First, an increase in the transcription of a number of pro-inflammatory cytokines and chemokines, such as TNF-α, IL-1β, IL-1α, and members of the SCY family of proteins, was evident that may constitute a general host recruitment of antibacterial defenses. Alternatively, Brucella may subvert newly arriving macrophages for additional intracellular infection. Second, transcription of receptors and cytokines associated with antigen presentation, e.g., MHC class II and IL-12p40, were not evident at this 4 hour period of infection. Third, Brucella inhibited transcription of various host genes involved in apoptosis, cell cycling, and intracellular vesicular trafficking. Identification of macrophage genes whose transcription was inhibited suggests that Brucella utilizes specific mechanisms to target certain cell pathways. In conclusion, these data suggest that B. abortus can alter macrophage pathways to recruit additional macrophages for future infection while simultaneously inhibiting apoptosis and innate immune mechanisms within the macrophage permitting intracellular survival of the bacterium. These results provide insights into the pathogenic strategies used by Brucella to survive long-term within a hostile environment.


systematic_name: M5758
exact_source: GSE8384_1759_200_DN
source_species_code: MM
GEO_id: GSE8384
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of control RAW264.7 cells (macrophages) versus those infected with B. abortus.

description_full:
  Identification of host responses at the gene transcription level provides a molecular profile of the events that occur following infection. Brucella abortus is a facultative intracellular pathogen of macrophages that induces chronic infection in humans and domestic animals. Using microarray technology, the response of macrophages 4 hours following B. abortus infection was analyzed to identify early intracellular infection events that occur in macrophages. Of the more than 6,000 genes, we identified over 140 genes that were reproducibly differentially transcribed. First, an increase in the transcription of a number of pro-inflammatory cytokines and chemokines, such as TNF-α, IL-1β, IL-1α, and members of the SCY family of proteins, was evident that may constitute a general host recruitment of antibacterial defenses. Alternatively, Brucella may subvert newly arriving macrophages for additional intracellular infection. Second, transcription of receptors and cytokines associated with antigen presentation, e.g., MHC class II and IL-12p40, were not evident at this 4 hour period of infection. Third, Brucella inhibited transcription of various host genes involved in apoptosis, cell cycling, and intracellular vesicular trafficking. Identification of macrophage genes whose transcription was inhibited suggests that Brucella utilizes specific mechanisms to target certain cell pathways. In conclusion, these data suggest that B. abortus can alter macrophage pathways to recruit additional macrophages for future infection while simultaneously inhibiting apoptosis and innate immune mechanisms within the macrophage permitting intracellular survival of the bacterium. These results provide insights into the pathogenic strategies used by Brucella to survive long-term within a hostile environment.


description_brief: Genes up-regulated in comparison of untreated macrophages versus those treated with IL1.
systematic_name: M5759
exact_source: GSE8515_1721_200_UP
source_species_code: HS
GEO_id: GSE8515
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Using whole-genome Affymetrix microarrays (HG-U133A), we characterized the transcriptome profile of cultured human macrophages stimulated for 4 h with interleukin 1 (IL-1) or interleukin 6 (IL-6). We found that, in distinction to liver cells, IL-1 is much more potent than IL-6 in modifying macrophage gene expression, although considerable heterogeneity in response of macrophages deriving from individual blood donors was observed. The obtained results permitted to identify a large number of cytokine-responsive genes. coding for proteins of unknown function that are now being studied in our laboratory. They may represent novel targets in the anti-inflammatory therapy.


systematic_name: M5763
exact_source: GSE8515_1722_200_UP
source_species_code: HS
GEO_id: GSE8515
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages versus those treated with IL6 [GeneID=3569].

description_full:
  Using whole-genome Affymetrix microarrays (HG-U133A), we characterized the transcriptome profile of cultured human macrophages stimulated for 4 h with interleukin 1 (IL-1) or interleukin 6 (IL-6). We found that, in distinction to liver cells, IL-1 is much more potent than IL-6 in modifying macrophage gene expression, although considerable heterogeneity in response of macrophages deriving from individual blood donors was observed. The obtained results permitted to identify a large number of cytokine-responsive genes. coding for proteins of unknown function that are now being studied in our laboratory. They may represent novel targets in the anti-inflammatory therapy.


systematic_name: M5765
exact_source: GSE8515_1722_200_DN
source_species_code: HS
GEO_id: GSE8515
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages versus those treated with IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5766
exact_source: GSE8515_1723_200_UP
source_species_code: HS
GEO_id: GSE8515
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages versus those treated with IL1 and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5767
exact_source: GSE8515_1723_200_DN
source_species_code: HS
GEO_id: GSE8515
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages versus those treated with IL1 and IL6 [GeneID=3569].

description_full:
[cell repeats an earlier one in this file: 674 characters]


systematic_name: M5769
exact_source: GSE8678_1059_200_UP
source_species_code: MM
GEO_id: GSE8678
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in IL7R [GeneID=3575] low effector CD8 T cells versus IL7R [GeneID=3575] high effector CD8 T cells.

description_full:
  At the peak of the CD8 T cell response to acture viral and bacterial infections, expression of the Interleukin-7 Receptor (IL-7R) marks Memory Precursor Effector CD8 T Cells (MPECs) from other Short-Lived Effector CD8 T cells (SLECs), which are IL-7Rlo. This study was designed to determine the gene expression differences between these two subsets of effector CD8 T cells.


systematic_name: M5771
exact_source: GSE8678_1059_200_DN
source_species_code: MM
GEO_id: GSE8678
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in IL7R [GeneID=3575] low effector CD8 T cells versus IL7R [GeneID=3575] high effector CD8 T cells.

description_full:
  At the peak of the CD8 T cell response to acture viral and bacterial infections, expression of the Interleukin-7 Receptor (IL-7R) marks Memory Precursor Effector CD8 T Cells (MPECs) from other Short-Lived Effector CD8 T cells (SLECs), which are IL-7Rlo. This study was designed to determine the gene expression differences between these two subsets of effector CD8 T cells.


description_brief: Genes up-regulated in dendritic cells (DC) from spleen versus those from intestine.
systematic_name: M5772
exact_source: GSE8868_1524_200_UP
source_species_code: MM
GEO_id: GSE8868
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The intestinal immune system must elicit robust immunity against harmful pathogens but restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood. Here we describe a population of CD11b+F4/80+CD11c– macrophages in the lamina propria (LP) that express several anti-inflammatory molecules including interleukin 10 (IL-10), but little or no pro-inflammatory cytokines, even upon stimulation with Toll-like receptor (TLR) ligands. These macrophages induced, in a manner dependent on IL-10, retinoic acid and exogenous transforming growth factor-β, differentiation of FoxP3+ regulatory T cells. In contrast, LP CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by LP macrophages, indicating that a dynamic interplay between these subsets may influence the balance between immune activation and tolerance. Splenic or small intestine lamina propria CD11b+11c- cells were isolated for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine the unique genetic profile of small intestine lamina propria CD11b+11c- cells.


systematic_name: M5774
exact_source: GSE9006_2237_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at the time of diagnosis.

description_full:
  Objective: We hypothesized that type 1 diabetes (T1D) is accompanied by changes in gene expression in peripheral blood mononuclear cells (PBMCs) due to dysregulation of adaptive and innate immunity, counterregulatory responses to immune dysregulation, insulin deficiency and hyperglycemia. Research Design and Methods: Microarray analysis was performed on PBMCs from 43 patients with newly diagnosed T1D, 12 patients with newly diagnosed type 2 diabetes (T2D) and 24 healthy controls. One and four month follow-up samples were obtained from 20 of the T1D patients. Results: Microarray analysis identified 282 genes differing in expression between newlydiagnosed T1D patients and controls at a false discovery rate of 0.05. Changes in expression of interleukin-1β (IL1B), early growth response gene 3 (EGR3), and prostaglandin-endoperoxide synthase 2 (PTGS2) resolved within four months of insulin therapy and were also observed in T2D suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81/282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly-connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D. Conclusion: T1D and T2D likely share a final common pathway for beta cell dysfunction that includes secretion of interleukin-1β and prostaglandins by immune effector cells, exacerbating existing beta cell dysfunction, and causing further hyperglycemia. The results identify several targets for disease-modifying therapy of diabetes and potential biomarkers for monitoring treatment efficacy.


systematic_name: M5776
exact_source: GSE9006_2237_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at the time of diagnosis.

description_full:
  Objective: We hypothesized that type 1 diabetes (T1D) is accompanied by changes in gene expression in peripheral blood mononuclear cells (PBMCs) due to dysregulation of adaptive and innate immunity, counterregulatory responses to immune dysregulation, insulin deficiency and hyperglycemia. Research Design and Methods: Microarray analysis was performed on PBMCs from 43 patients with newly diagnosed T1D, 12 patients with newly diagnosed type 2 diabetes (T2D) and 24 healthy controls. One and four month follow-up samples were obtained from 20 of the T1D patients. Results: Microarray analysis identified 282 genes differing in expression between newlydiagnosed T1D patients and controls at a false discovery rate of 0.05. Changes in expression of interleukin-1β (IL1B), early growth response gene 3 (EGR3), and prostaglandin-endoperoxide synthase 2 (PTGS2) resolved within four months of insulin therapy and were also observed in T2D suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81/282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly-connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D. Conclusion: T1D and T2D likely share a final common pathway for beta cell dysfunction that includes secretion of interleukin-1β and prostaglandins by immune effector cells, exacerbating existing beta cell dysfunction, and causing further hyperglycemia. The results identify several targets for disease-modifying therapy of diabetes and potential biomarkers for monitoring treatment efficacy.


systematic_name: M5777
exact_source: GSE9006_2238_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at 1 month after the diagnosis.

description_full:
  Objective: We hypothesized that type 1 diabetes (T1D) is accompanied by changes in gene expression in peripheral blood mononuclear cells (PBMCs) due to dysregulation of adaptive and innate immunity, counterregulatory responses to immune dysregulation, insulin deficiency and hyperglycemia. Research Design and Methods: Microarray analysis was performed on PBMCs from 43 patients with newly diagnosed T1D, 12 patients with newly diagnosed type 2 diabetes (T2D) and 24 healthy controls. One and four month follow-up samples were obtained from 20 of the T1D patients. Results: Microarray analysis identified 282 genes differing in expression between newlydiagnosed T1D patients and controls at a false discovery rate of 0.05. Changes in expression of interleukin-1β (IL1B), early growth response gene 3 (EGR3), and prostaglandin-endoperoxide synthase 2 (PTGS2) resolved within four months of insulin therapy and were also observed in T2D suggesting that they resulted from hyperglycemia. With use of a knowledge base, 81/282 genes could be placed within a network of interrelated genes with predicted functions including apoptosis and cell proliferation. IL1B and the MYC oncogene were the most highly-connected genes in the network. IL1B was highly overexpressed in both T1D and T2D, whereas MYC was dysregulated only in T1D. Conclusion: T1D and T2D likely share a final common pathway for beta cell dysfunction that includes secretion of interleukin-1β and prostaglandins by immune effector cells, exacerbating existing beta cell dysfunction, and causing further hyperglycemia. The results identify several targets for disease-modifying therapy of diabetes and potential biomarkers for monitoring treatment efficacy.


systematic_name: M5778
exact_source: GSE9006_2238_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at 1 month after the diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5779
exact_source: GSE9006_2239_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at 4  month after the diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5780
exact_source: GSE9006_2239_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 1 diabetes at 4  month after the diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5781
exact_source: GSE9006_2240_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 2 diabetes at the time of diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5782
exact_source: GSE9006_2240_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from healthy donors versus PBMCs from patients with type 2 diabetes at the time of diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5783
exact_source: GSE9006_2241_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of the diagnosis versus those at 1 month later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5786
exact_source: GSE9006_2241_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of the diagnosis versus those at 1 month later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5787
exact_source: GSE9006_2242_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of the diagnosis versus those at 4 months later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5788
exact_source: GSE9006_2242_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of the diagnosis versus those at 4 months later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5790
exact_source: GSE9006_2243_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at 1 month after the diagnosis versus those at 4 months later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5791
exact_source: GSE9006_2243_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at 1 month after the diagnosis versus those at 4 months later.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5797
exact_source: GSE9006_2244_200_UP
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of diagnosis versus those with type 2 diabetes at the time of diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5799
exact_source: GSE9006_2244_200_DN
source_species_code: HS
GEO_id: GSE9006
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in peripheral blood mononuclear cells (PBMC) from patients with type 1 diabetes at the time of diagnosis versus those with type 2 diabetes at the time of diagnosis.

description_full:
[cell repeats an earlier one in this file: 1715 characters]


systematic_name: M5800
exact_source: GSE9037_1743_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages at 4 h versus those treated with LPS (TLR4 agonist) at 1 h.

description_full:
  IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of bone marrow macrophages obtained from WT and IRAK-4 KD mice with a number of experimental techniques demonstrated that the IRAK-4 KD cells greatly lack responsiveness to stimulation with the Toll-like receptor 4 (TLR4) agonist LPS. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent LPS response genes and revealed that the induction of LPS-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in TLR4-mediated induction of inflammatory responses.


systematic_name: M5801
exact_source: GSE9037_1743_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages at 4 h versus those treated with LPS (TLR4 agonist) at 1 h.

description_full:
  IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of bone marrow macrophages obtained from WT and IRAK-4 KD mice with a number of experimental techniques demonstrated that the IRAK-4 KD cells greatly lack responsiveness to stimulation with the Toll-like receptor 4 (TLR4) agonist LPS. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent LPS response genes and revealed that the induction of LPS-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in TLR4-mediated induction of inflammatory responses.


systematic_name: M5803
exact_source: GSE9037_1744_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages at 4 h versus those treated with LPS (TLR4 agonist) at 4 h.

description_full:
  IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of bone marrow macrophages obtained from WT and IRAK-4 KD mice with a number of experimental techniques demonstrated that the IRAK-4 KD cells greatly lack responsiveness to stimulation with the Toll-like receptor 4 (TLR4) agonist LPS. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent LPS response genes and revealed that the induction of LPS-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in TLR4-mediated induction of inflammatory responses.


systematic_name: M5806
exact_source: GSE9037_1744_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages at 4 h versus those treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5807
exact_source: GSE9037_1745_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages from IRAK4 [GeneID=51135] deficient mice  at 4 h versus those treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5808
exact_source: GSE9037_1745_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages from IRAK4 [GeneID=51135] deficient mice  at 4 h versus those treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5809
exact_source: GSE9037_1746_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated macrophages from IRAK4 [GeneID=51135] deficient mice  at 4 h versus those treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5811
exact_source: GSE9037_1746_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated macrophages from IRAK4 [GeneID=51135] deficient mice  at 4 h versus those treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5812
exact_source: GSE9037_1747_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated wild type macrophages at 4 h versus those from IRAK4 [GeneID=51135] deficient mice at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5814
exact_source: GSE9037_1747_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated wild type macrophages at 4 h versus those from IRAK4 [GeneID=51135] deficient mice at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5815
exact_source: GSE9037_1748_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of untreated wild type macrophages at 1 h versus those from IRAK4 [GeneID=51135] deficient mice treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5816
exact_source: GSE9037_1748_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of untreated wild type macrophages at 1 h versus those from IRAK4 [GeneID=51135] deficient mice treated with LPS (TLR4 agonist) at 1 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5817
exact_source: GSE9037_1749_200_UP
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of wild type macrophage treated with LPS (TLR4 agonist) at 4 h versus those from IRAK4 [GeneID=51135] deficient mice treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


systematic_name: M5818
exact_source: GSE9037_1749_200_DN
source_species_code: MM
GEO_id: GSE9037
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of wild type macrophage treated with LPS (TLR4 agonist) at 4 h versus those from IRAK4 [GeneID=51135] deficient mice treated with LPS (TLR4 agonist) at 4 h.

description_full:
[cell repeats an earlier one in this file: 1056 characters]


description_brief: Genes up-regulated in comparison of naive CD8 T cells versus effector CD8 T cells.
systematic_name: M5819
exact_source: GSE9650_1253_200_UP
source_species_code: MM
GEO_id: GSE9650
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  CD8 T cells normally differentiate from resting naïve T cells into function effector and then memory CD8 T cells following acute infections. During chronic viral infections, however, virus-specific CD8 T cells often become exhausted. We used microarrays to examine the gene expression differences between naive, effector, memory and exhausted virus-specific CD8 T cells following lymphocytic choriomeningitis virus infection.


systematic_name: M5842
exact_source: GSE9650_1259_200_UP
source_species_code: MM
GEO_id: GSE9650
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of virus specific (gp33) exhausted CD8 T cells versus the virus specific (gp276) cells.

description_full:
[cell repeats an earlier one in this file: 425 characters]


systematic_name: M5843
exact_source: GSE9650_1259_200_DN
source_species_code: MM
GEO_id: GSE9650
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of virus specific (gp33) exhausted CD8 T cells versus the virus specific (gp276) cells.

description_full:
[cell repeats an earlier one in this file: 425 characters]


systematic_name: M5844
exact_source: GSE9988_2034_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with 5000 ng/ml LPS (TLR4 agonist).

description_full:
  TREM-1 is an orphan immunoreceptor expressed on monocytes, macrophages, and neutrophils. TREM-1 associates with and signals via the adapter protein DAP12/TYROBP, which contains an immunoreceptor tyrosine-based activation motif (ITAM). TREM-1 activation by receptor cross-linking is pro-inflammatory, and can amplify cellular responses to Toll-like receptor (TLR) ligands such as bacterial lipopolysaccharide (LPS). To investigate the cellular consequences of TREM-1 activation, we have characterized global gene expression changes in human monocytes in response to TREM-1 cross-linking in comparison to and combined with LPS. Both TREM-1 activation and LPS up-regulate chemokines, cytokines, matrix metalloproteases, and PTGS/COX2, consistent with a core inflammatory response. However, other immunomodulatory factors are selectively induced, including SPP1 and CSF1 (i.e., M-CSF) by TREM-1 activation and IL-23 and CSF3 (i.e., G-CSF) by LPS. Additionally, cross-talk between TREM-1 activation and LPS occurs on multiple levels. While synergy in GM-CSF protein production is reflected in commensurate mRNA abundance, comparable synergy in IL-1b protein production is not. TREM-1 activation also attenuates the induction of some LPS target genes, including those that encode IL-12 cytokine family subunits. Whereas positive TREM-1 outputs are abolished by the PI3K inhibitor wortmannin, this attenuation is largely PI3K-independent. These experiments provide a detailed analysis of the cellular consequences of TREM-1 activation, and highlight some of the complexity in signal integration between ITAM- and TLR-mediated signaling.


systematic_name: M5845
exact_source: GSE9988_2034_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with 5000 ng/ml LPS (TLR4 agonist).

description_full:
  TREM-1 is an orphan immunoreceptor expressed on monocytes, macrophages, and neutrophils. TREM-1 associates with and signals via the adapter protein DAP12/TYROBP, which contains an immunoreceptor tyrosine-based activation motif (ITAM). TREM-1 activation by receptor cross-linking is pro-inflammatory, and can amplify cellular responses to Toll-like receptor (TLR) ligands such as bacterial lipopolysaccharide (LPS). To investigate the cellular consequences of TREM-1 activation, we have characterized global gene expression changes in human monocytes in response to TREM-1 cross-linking in comparison to and combined with LPS. Both TREM-1 activation and LPS up-regulate chemokines, cytokines, matrix metalloproteases, and PTGS/COX2, consistent with a core inflammatory response. However, other immunomodulatory factors are selectively induced, including SPP1 and CSF1 (i.e., M-CSF) by TREM-1 activation and IL-23 and CSF3 (i.e., G-CSF) by LPS. Additionally, cross-talk between TREM-1 activation and LPS occurs on multiple levels. While synergy in GM-CSF protein production is reflected in commensurate mRNA abundance, comparable synergy in IL-1b protein production is not. TREM-1 activation also attenuates the induction of some LPS target genes, including those that encode IL-12 cytokine family subunits. Whereas positive TREM-1 outputs are abolished by the PI3K inhibitor wortmannin, this attenuation is largely PI3K-independent. These experiments provide a detailed analysis of the cellular consequences of TREM-1 activation, and highlight some of the complexity in signal integration between ITAM- and TLR-mediated signaling.


systematic_name: M5846
exact_source: GSE9988_2035_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with 1 ng/ml LPS (TLR4 agonist).

description_full:
  TREM-1 is an orphan immunoreceptor expressed on monocytes, macrophages, and neutrophils. TREM-1 associates with and signals via the adapter protein DAP12/TYROBP, which contains an immunoreceptor tyrosine-based activation motif (ITAM). TREM-1 activation by receptor cross-linking is pro-inflammatory, and can amplify cellular responses to Toll-like receptor (TLR) ligands such as bacterial lipopolysaccharide (LPS). To investigate the cellular consequences of TREM-1 activation, we have characterized global gene expression changes in human monocytes in response to TREM-1 cross-linking in comparison to and combined with LPS. Both TREM-1 activation and LPS up-regulate chemokines, cytokines, matrix metalloproteases, and PTGS/COX2, consistent with a core inflammatory response. However, other immunomodulatory factors are selectively induced, including SPP1 and CSF1 (i.e., M-CSF) by TREM-1 activation and IL-23 and CSF3 (i.e., G-CSF) by LPS. Additionally, cross-talk between TREM-1 activation and LPS occurs on multiple levels. While synergy in GM-CSF protein production is reflected in commensurate mRNA abundance, comparable synergy in IL-1b protein production is not. TREM-1 activation also attenuates the induction of some LPS target genes, including those that encode IL-12 cytokine family subunits. Whereas positive TREM-1 outputs are abolished by the PI3K inhibitor wortmannin, this attenuation is largely PI3K-independent. These experiments provide a detailed analysis of the cellular consequences of TREM-1 activation, and highlight some of the complexity in signal integration between ITAM- and TLR-mediated signaling.


systematic_name: M5847
exact_source: GSE9988_2035_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with 1 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5848
exact_source: GSE9988_2036_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5849
exact_source: GSE9988_2036_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5850
exact_source: GSE9988_2037_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5851
exact_source: GSE9988_2037_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5852
exact_source: GSE9988_2038_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5853
exact_source: GSE9988_2038_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5854
exact_source: GSE9988_2039_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus those treated with 1 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5855
exact_source: GSE9988_2039_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus those treated with 1 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5856
exact_source: GSE9988_2040_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with anti-TREM1 [GeneID=54210].

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5857
exact_source: GSE9988_2040_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with anti-TREM1 [GeneID=54210].

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5858
exact_source: GSE9988_2041_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5859
exact_source: GSE9988_2041_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5860
exact_source: GSE9988_2042_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5861
exact_source: GSE9988_2042_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5862
exact_source: GSE9988_2043_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5865
exact_source: GSE9988_2043_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist).

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5867
exact_source: GSE9988_2044_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5870
exact_source: GSE9988_2044_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5875
exact_source: GSE9988_2046_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5877
exact_source: GSE9988_2046_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist) versus monocytes treated with control IgG.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5878
exact_source: GSE9988_2047_200_UP
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist) versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


systematic_name: M5879
exact_source: GSE9988_2047_200_DN
source_species_code: HS
GEO_id: GSE9988
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in comparison of monocytes treated with anti-TREM1 [GeneID=54210] and 5000 ng/ml LPS (TLR4 agonist) versus untreated monocytes.

description_full:
[cell repeats an earlier one in this file: 1629 characters]


description_brief: Genes up-regulated in livers: SOCS3 [GeneID=9021] knockout versus wildtype.
systematic_name: M5960
exact_source: GSE369_2900_200_UP
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection. Either interferon-gamma-/-, albumin-cre(-) Socs3(w/fl) mice, or albumin-cre(+) Socs3(-/fl) mice were injected with either phosphate-buffered saline, interferon-gamma, or interfeukin-6, and livers taken after 4h.


systematic_name: M5964
exact_source: GSE369_2906_200_UP
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in livers injected with IL6 [GeneID=3569]: SOCS3 [GeneID=9021] knockout versus wildtype.

description_full:
  Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection. Either interferon-gamma-/-, albumin-cre(-) Socs3(w/fl) mice, or albumin-cre(+) Socs3(-/fl) mice were injected with either phosphate-buffered saline, interferon-gamma, or interfeukin-6, and livers taken after 4h.


systematic_name: M5966
exact_source: GSE369_2906_200_DN
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in livers injected with IL6 [GeneID=3569]: SOCS3 [GeneID=9021] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 294 characters]


systematic_name: M5973
exact_source: GSE369_2904_200_UP
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in liver from SOC3 [GeneID=9021] knockout: untreated versus IL6 [GeneID=3569] injection.

description_full:
[cell repeats an earlier one in this file: 294 characters]


systematic_name: M5975
exact_source: GSE369_2904_200_DN
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in liver from SOC3 [GeneID=9021] knockout: untreated versus IL6 [GeneID=3569] injection.

description_full:
[cell repeats an earlier one in this file: 294 characters]


systematic_name: M5976
exact_source: GSE369_2903_200_UP
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in liver from SOCS3 [GeneID=9021] knockout: untreated versus IL6 [GeneID=3569] injection.

description_full:
[cell repeats an earlier one in this file: 294 characters]


systematic_name: M5977
exact_source: GSE369_2903_200_DN
source_species_code: MM
GEO_id: GSE369
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in liver from SOCS3 [GeneID=9021] knockout: untreated versus IL6 [GeneID=3569] injection.

description_full:
[cell repeats an earlier one in this file: 294 characters]


systematic_name: M5984
exact_source: GSE411_2908_200_DN
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages treated by IL6 [GeneID=3569] for 400min: wildtype versus SOCS3 [GeneID=9021].

description_full:
  Effects of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6. Fetal liver cells from SOCS3+/+ or SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Macrophages were either unstimulated, or stimulated for 100 or 400 minutes with 10 ng/ml IL-6.


systematic_name: M5992
exact_source: GSE411_2907_200_UP
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages treated by IL6 [GeneID=3569] for 100min: wildtype versus SOCS3 [GeneID=9021].

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M5993
exact_source: GSE411_2907_200_DN
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages treated by IL6 [GeneID=3569] for 100min: wildtype versus SOCS3 [GeneID=9021].

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M5994
exact_source: GSE411_2908_200_UP
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages treated by IL6 [GeneID=3569] for 400min: wildtype versus SOCS3 [GeneID=9021].

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M5995
exact_source: GSE411_2914_200_DN
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with SOCS3 [GeneID=9021] knockout treated by IL6 [GeneID=3569]: 100min versus 400min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M6000
exact_source: GSE411_2912_200_DN
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with SOCS3 [GeneID=9021]: untreated versus IL6 [GeneID=3569] for 100min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M6001
exact_source: GSE411_2913_200_UP
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with SOCS3 [GeneID=9021]: untreated versus IL6 [GeneID=3569] for 400min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M6003
exact_source: GSE411_2913_200_DN
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages with SOCS3 [GeneID=9021]: untreated versus IL6 [GeneID=3569] for 400min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M6004
exact_source: GSE411_2912_200_UP
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with SOCS3 [GeneID=9021]: untreated versus IL6 [GeneID=3569] for 100min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


systematic_name: M6005
exact_source: GSE411_2914_200_UP
source_species_code: MM
GEO_id: GSE411
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages with SOCS3 [GeneID=9021] knockout treated by IL6 [GeneID=3569]: 100min versus 400min.

description_full:
[cell repeats an earlier one in this file: 358 characters]


description_brief: Genes up-regulated in dendritic cells: wildtype versus CIITA [GeneID=4261] knockout.
systematic_name: M6006
exact_source: GSE557_2915_200_UP
source_species_code: MM
GEO_id: GSE557
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Triplicates preparations of RNA from day 10 DC's. Experiment is described in Wong et al 2003 Nat. Immunol.


systematic_name: M6015
exact_source: GSE2770_2759_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (2h).

description_full:
  Th1 and Th2 cells arise from a common precursor cell in response to triggering through the TCR and cytokine receptors for IL-12 or IL-4. This leads to activation of complex signaling pathways, which are not known in detail. Disturbances in the balance between type 1 and type 2 responses can lead to certain immune-mediated diseases. Thus, it is important to understand how Th1 and Th2 cells are generated. To clarify the mechanisms as to how IL-12 and IL-4 induce Th1 and Th2 differentiation and how TGF-beta can inhibit this process, we have used oligonucleotide arrays to examine the early polarization of Th1 and Th2 cells in the presence and absence of TGF-beta after 0, 2, 6 and 48 hours of polarization.


systematic_name: M6016
exact_source: GSE2770_2759_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (2h).

description_full:
  Th1 and Th2 cells arise from a common precursor cell in response to triggering through the TCR and cytokine receptors for IL-12 or IL-4. This leads to activation of complex signaling pathways, which are not known in detail. Disturbances in the balance between type 1 and type 2 responses can lead to certain immune-mediated diseases. Thus, it is important to understand how Th1 and Th2 cells are generated. To clarify the mechanisms as to how IL-12 and IL-4 induce Th1 and Th2 differentiation and how TGF-beta can inhibit this process, we have used oligonucleotide arrays to examine the early polarization of Th1 and Th2 cells in the presence and absence of TGF-beta after 0, 2, 6 and 48 hours of polarization.


systematic_name: M6017
exact_source: GSE2770_2772_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (6h).

description_full:
  Th1 and Th2 cells arise from a common precursor cell in response to triggering through the TCR and cytokine receptors for IL-12 or IL-4. This leads to activation of complex signaling pathways, which are not known in detail. Disturbances in the balance between type 1 and type 2 responses can lead to certain immune-mediated diseases. Thus, it is important to understand how Th1 and Th2 cells are generated. To clarify the mechanisms as to how IL-12 and IL-4 induce Th1 and Th2 differentiation and how TGF-beta can inhibit this process, we have used oligonucleotide arrays to examine the early polarization of Th1 and Th2 cells in the presence and absence of TGF-beta after 0, 2, 6 and 48 hours of polarization.


systematic_name: M6018
exact_source: GSE2770_2772_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6019
exact_source: GSE2770_2760_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6020
exact_source: GSE2770_2771_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6021
exact_source: GSE2770_2769_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6022
exact_source: GSE2770_2770_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6024
exact_source: GSE2770_2770_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6025
exact_source: GSE2770_2771_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6027
exact_source: GSE2770_2798_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus TGFB1 [GeneID=7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6028
exact_source: GSE2770_2798_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus TGFB1 [GeneID=7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6029
exact_source: GSE2770_2799_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6030
exact_source: GSE2770_2799_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6032
exact_source: GSE2770_2800_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6033
exact_source: GSE2770_2800_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6035
exact_source: GSE2770_2801_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6037
exact_source: GSE2770_2768_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6038
exact_source: GSE2770_2769_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6039
exact_source: GSE2770_2802_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6040
exact_source: GSE2770_2803_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6042
exact_source: GSE2770_2803_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6043
exact_source: GSE2770_2763_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6044
exact_source: GSE2770_2764_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6045
exact_source: GSE2770_2764_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6047
exact_source: GSE2770_2765_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6048
exact_source: GSE2770_2765_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6049
exact_source: GSE2770_2766_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6053
exact_source: GSE2770_2766_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6055
exact_source: GSE2770_2767_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6056
exact_source: GSE2770_2767_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 [GeneID=7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6057
exact_source: GSE2770_2768_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6059
exact_source: GSE2770_2788_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus TGFB1 [GeneID=7040] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6060
exact_source: GSE2770_2788_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus TGFB1 [GeneID=7040] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6061
exact_source: GSE2770_2789_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6062
exact_source: GSE2770_2789_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6063
exact_source: GSE2770_2790_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6064
exact_source: GSE2770_2790_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6065
exact_source: GSE2770_2791_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6066
exact_source: GSE2770_2791_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6067
exact_source: GSE2770_2792_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6068
exact_source: GSE2770_2792_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6069
exact_source: GSE2770_2773_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6073
exact_source: GSE2770_2773_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6074
exact_source: GSE2770_2774_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6075
exact_source: GSE2770_2774_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6076
exact_source: GSE2770_2775_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6077
exact_source: GSE2770_2775_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6079
exact_source: GSE2770_2776_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6080
exact_source: GSE2770_2776_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6081
exact_source: GSE2770_2777_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6082
exact_source: GSE2770_2777_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6083
exact_source: GSE2770_2778_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6084
exact_source: GSE2770_2778_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus TGFB1 [GeneID=7040] and IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6085
exact_source: GSE2770_2779_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6086
exact_source: GSE2770_2779_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6087
exact_source: GSE2770_2760_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6088
exact_source: GSE2770_2761_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6089
exact_source: GSE2770_2761_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by TGFB1 and IL4 [GeneID=7040;3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6090
exact_source: GSE2770_2762_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6091
exact_source: GSE2770_2762_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6092
exact_source: GSE2770_2763_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells: untreated (0h) versus activated by anti-CD3 and anti-CD28 and then stimulated by IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6094
exact_source: GSE2770_2783_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6095
exact_source: GSE2770_2783_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6096
exact_source: GSE2770_2784_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6098
exact_source: GSE2770_2784_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6099
exact_source: GSE2770_2785_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus TGFB1 [GeneID=7050] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6102
exact_source: GSE2770_2785_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus TGFB1 [GeneID=7050] and IL-12 (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6103
exact_source: GSE2770_2786_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6104
exact_source: GSE2770_2786_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus IL4 [GeneID=3565] (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6106
exact_source: GSE2770_2787_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6107
exact_source: GSE2770_2787_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6108
exact_source: GSE2770_2794_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6109
exact_source: GSE2770_2795_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus TGFB1 [GeneID-7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6111
exact_source: GSE2770_2795_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus TGFB1 [GeneID-7040] and IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6112
exact_source: GSE2770_2796_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6114
exact_source: GSE2770_2796_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6115
exact_source: GSE2770_2797_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6118
exact_source: GSE2770_2797_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6119
exact_source: GSE2770_2793_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6120
exact_source: GSE2770_2794_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 and IL4 [GeneID=7040;3565] (48h) versus IL-12 (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6123
exact_source: GSE2770_2781_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6124
exact_source: GSE2770_2793_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL4 [GeneID=3565] (6h) versus untreated (6h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6125
exact_source: GSE2770_2782_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6126
exact_source: GSE2770_2782_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6127
exact_source: GSE2770_2780_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6128
exact_source: GSE2770_2781_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (2h) versus IL4 [GeneID=3565] (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6129
exact_source: GSE2770_2801_200_DN
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (48h) versus IL4 [GeneID=3565] (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6130
exact_source: GSE2770_2780_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: IL-12 (2h) versus untreated (2h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


systematic_name: M6131
exact_source: GSE2770_2802_200_UP
source_species_code: HS
GEO_id: GSE2770
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells activated by anti-CD3 and anti-CD28: TGFB1 [GeneID=7040] and IL-12 (48h) versus untreated (48h).

description_full:
[cell repeats an earlier one in this file: 710 characters]


description_brief: Genes up-regulated in mouse embryonic fibroblasts (MEF): untreated versus interferon beta.
systematic_name: M6133
exact_source: GSE3400_3548_200_UP
source_species_code: MM
GEO_id: GSE3400
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  A number of IFN-induced proteins are believed to be responsible for the antiviral state induced by IFNs. Our microarray analysis of IFN-regulated genes in MEFs from wild-type mice identified 124 probe sets that were differentially regulated upon IFN treatment. This group consisted of many known ISGs such as Ifit1, Gbp2, mx1, Isg15, Stat1, nmi, mx2, If204, Adar, Irf1, and protein kinase R.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6138
exact_source: GSE1112_2933_200_DN
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 alphabeta HY thymocyte RTOC culture versus CD8 alphaalpha HY thymocyte RTOC culture.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6140
exact_source: GSE1112_2931_200_UP
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 alphabeta OT1 thymocyte RTOC culture versus CD8 alphabeta HY thymocyte RTOC culture.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6141
exact_source: GSE1112_2932_200_UP
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 alphabeta OT1 thymocyte RTOC culture versus CD8 alphaalpha HY thymocyte RTOC culture.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6142
exact_source: GSE1112_2932_200_DN
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 alphabeta OT1 thymocyte RTOC culture versus CD8 alphaalpha HY thymocyte RTOC culture.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6143
exact_source: GSE1112_2933_200_UP
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 alphabeta HY thymocyte RTOC culture versus CD8 alphaalpha HY thymocyte RTOC culture.


description_full: Four independent chip hybridization with RNAs from four independent RTOC cultures.
systematic_name: M6146
exact_source: GSE1112_2931_200_DN
source_species_code: MM
GEO_id: GSE1112
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 alphabeta OT1 thymocyte RTOC culture versus CD8 alphabeta HY thymocyte RTOC culture.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6147
exact_source: GSE1740_2639_200_DN
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived macrophages: no priming, stimulated by interferon alpha versus primed by IFNG [GeneID=3458] and then stimulated by interferon alpha.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6148
exact_source: GSE1740_2636_200_UP
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived macrophages: untreated versus stimulated by interferon alpha.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6150
exact_source: GSE1740_2636_200_DN
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived macrophages: untreated versus stimulated by interferon alpha.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6152
exact_source: GSE1740_2637_200_DN
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived macrophages primed by IFNG [GeneID=3458]: untreated versus interferon alpha.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6157
exact_source: GSE1740_2638_200_DN
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived macrophages: no priming versus primed by IFNG [GeneID=3458].


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6158
exact_source: GSE1740_2639_200_UP
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived macrophages: no priming, stimulated by interferon alpha versus primed by IFNG [GeneID=3458] and then stimulated by interferon alpha.


description_full: Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
systematic_name: M6159
exact_source: GSE1740_2637_200_UP
source_species_code: HS
GEO_id: GSE1740
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived macrophages primed by IFNG [GeneID=3458]: untreated versus interferon alpha.


description_brief: Genes down-regulated in D10.G4.1 T cell line (3h): control versus treated with NMU [GeneID=10874].
systematic_name: M6160
exact_source: GSE1791_2959_200_DN
source_species_code: MM
GEO_id: GSE1791
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Effects of Neuromedin-U on gene expression in mouse D10.G4.1 T-cells natively expressing the GPCR Axor13


systematic_name: M6163
exact_source: GSE1791_2958_200_DN
source_species_code: MM
GEO_id: GSE1791
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in D10.G4.1 T cell line (0.8h): control versus treated with NMU [GeneID=10874].

description_full:
  Effects of Neuromedin-U on gene expression in mouse D10.G4.1 T-cells natively expressing the GPCR Axor13


systematic_name: M6174
exact_source: GSE2128_2392_200_DN
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
  Fetal thymic organ culture (FTOC) DC2.5 CD4+CD8+ thymocytes from B6g7 or NOD background. 0 or 16 hour after addition of the BDC mimitope


systematic_name: M6180
exact_source: GSE2128_2391_200_UP
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
  Fetal thymic organ culture (FTOC) DC2.5 CD4+CD8+ thymocytes from B6g7 or NOD background. 0 or 16 hour after addition of the BDC mimitope


systematic_name: M6182
exact_source: GSE2128_2394_200_DN
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6183
exact_source: GSE2128_2393_200_UP
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6185
exact_source: GSE2128_2391_200_DN
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6186
exact_source: GSE2128_2392_200_UP
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6187
exact_source: GSE2128_2393_200_DN
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with no peptide 0h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6188
exact_source: GSE2128_2394_200_UP
source_species_code: MM
GEO_id: GSE2128
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in C57BL6 CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h versus NOD CD4 CD8 double positive thymocyte transgenic for the BDC2.5 TCR incubated with mimetope negative sel 16h.

description_full:
[cell repeats an earlier one in this file: 136 characters]


systematic_name: M6190
exact_source: GSE2124_3055_200_DN
source_species_code: MM
GEO_id: GSE2124
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in mesenteric lymph nodes: control versus 1 day after injection with soluble form of LTB [GeneID=4050].

description_full:
  treatment of mesenteric lymph nodes with soluble lymphotoxin-beta receptor for 0,1,2,3,27 and 35 days


systematic_name: M6191
exact_source: GSE2124_3055_200_UP
source_species_code: MM
GEO_id: GSE2124
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in mesenteric lymph nodes: control versus 1 day after injection with soluble form of LTB [GeneID=4050].

description_full:
  treatment of mesenteric lymph nodes with soluble lymphotoxin-beta receptor for 0,1,2,3,27 and 35 days


description_brief: Genes up-regulated in polymorphonuclear leukocytes (9h): S. aureus infection versus control.
systematic_name: M6192
exact_source: GSE2405_3574_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Polymorphonuclear leukocytes (PMNs) were obtained from healthy individuals in accordance with protocols approved by the Institutional Review Board for Human Subjects at the University of Minnesota and the National Institute of Allergy and Infectious Diseases. PMNs (107) were combined on ice with live S. aureus (108) or with live or heat-killed A. phagocytophilum (bacteria isolated from 5x106 infected HL60 cells for a ratio of 1 infected HL60 cell: 2 PMNs, ~ 5-20 A. phagocytophilum: PMN) in wells of a 12-well tissue culture plate (pre-coated with 20% autologous normal human serum). Unstimulated control assays received either buffer (for S. aureus comparisons) or clarified HL60 lysate (for A. phagocytophilum comparisons). Plates were centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis and incubated at 37 deg. C in a CO2 incubator for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target was performed as described in Methods. Labeling of samples, hybridization of cRNA with HU133A oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols ( http://www.affymetrix.com/pdf/expression_manual.pdf ). Experiments were performed in triplicate, using PMNs from three healthy individuals for each treatment.


systematic_name: M6193
exact_source: GSE2405_3587_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (24h): control versus infection by A. phagocytophilum.

description_full:
  Polymorphonuclear leukocytes (PMNs) were obtained from healthy individuals in accordance with protocols approved by the Institutional Review Board for Human Subjects at the University of Minnesota and the National Institute of Allergy and Infectious Diseases. PMNs (107) were combined on ice with live S. aureus (108) or with live or heat-killed A. phagocytophilum (bacteria isolated from 5x106 infected HL60 cells for a ratio of 1 infected HL60 cell: 2 PMNs, ~ 5-20 A. phagocytophilum: PMN) in wells of a 12-well tissue culture plate (pre-coated with 20% autologous normal human serum). Unstimulated control assays received either buffer (for S. aureus comparisons) or clarified HL60 lysate (for A. phagocytophilum comparisons). Plates were centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis and incubated at 37 deg. C in a CO2 incubator for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target was performed as described in Methods. Labeling of samples, hybridization of cRNA with HU133A oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols ( http://www.affymetrix.com/pdf/expression_manual.pdf ). Experiments were performed in triplicate, using PMNs from three healthy individuals for each treatment.


systematic_name: M6194
exact_source: GSE2405_3588_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (9h) infection by A. phagocytophilum: heat killed versus live bacteria.

description_full:
  Polymorphonuclear leukocytes (PMNs) were obtained from healthy individuals in accordance with protocols approved by the Institutional Review Board for Human Subjects at the University of Minnesota and the National Institute of Allergy and Infectious Diseases. PMNs (107) were combined on ice with live S. aureus (108) or with live or heat-killed A. phagocytophilum (bacteria isolated from 5x106 infected HL60 cells for a ratio of 1 infected HL60 cell: 2 PMNs, ~ 5-20 A. phagocytophilum: PMN) in wells of a 12-well tissue culture plate (pre-coated with 20% autologous normal human serum). Unstimulated control assays received either buffer (for S. aureus comparisons) or clarified HL60 lysate (for A. phagocytophilum comparisons). Plates were centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis and incubated at 37 deg. C in a CO2 incubator for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target was performed as described in Methods. Labeling of samples, hybridization of cRNA with HU133A oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols ( http://www.affymetrix.com/pdf/expression_manual.pdf ). Experiments were performed in triplicate, using PMNs from three healthy individuals for each treatment.


systematic_name: M6196
exact_source: GSE2405_3588_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (9h) infection by A. phagocytophilum: heat killed versus live bacteria.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6197
exact_source: GSE2405_3586_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (12h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6198
exact_source: GSE2405_3590_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (9h): treated by heat killed HC60 cell (promyelocytic leukemia) lysate versus A. phagocytophilum infection.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6199
exact_source: GSE2405_3590_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (9h): treated by heat killed HC60 cell (promyelocytic leukemia) lysate versus A. phagocytophilum infection.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6200
exact_source: GSE2405_3591_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (24h): treated by heat killed HC60 cell (promyelocytic leukemia) lysate versus A. phagocytophilum infection.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6201
exact_source: GSE2405_3591_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (24h): treated by heat killed HC60 cell (promyelocytic leukemia) lysate versus A. phagocytophilum infection.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6202
exact_source: GSE2405_3585_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (9h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6203
exact_source: GSE2405_3586_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (12h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6204
exact_source: GSE2405_3587_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (24h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6207
exact_source: GSE2405_3575_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes 9h after infection by: S. aureus versus A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6208
exact_source: GSE2405_3575_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes 9h after infection by: S. aureus versus A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6209
exact_source: GSE2405_3582_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (1.5h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6211
exact_source: GSE2405_3582_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (1.5h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6212
exact_source: GSE2405_3583_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (3h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6213
exact_source: GSE2405_3583_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (3h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6214
exact_source: GSE2405_3584_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (6h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6215
exact_source: GSE2405_3584_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (6h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6217
exact_source: GSE2405_3585_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (9h): control versus infection by A. phagocytophilum.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6218
exact_source: GSE2405_3589_200_UP
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in polymorphonuclear leukocytes (24h) infection by A. phagocytophilum: heat killed versus live bacteria.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


systematic_name: M6219
exact_source: GSE2405_3589_200_DN
source_species_code: HS
GEO_id: GSE2405
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in polymorphonuclear leukocytes (24h) infection by A. phagocytophilum: heat killed versus live bacteria.

description_full:
[cell repeats an earlier one in this file: 1478 characters]


description_brief: Genes up-regulated in thymocytes: double negative versus double positive.
systematic_name: M6226
exact_source: GSE22601_3410_200_UP
source_species_code: HS
GEO_id: GSE22601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  T cells develop from progenitors that migrate from the bone marrow into the thymus. Thymocytes are subdivided roughly as being double negative (DN), double positive (DP), or single positive (SP), based on the expression of the CD4 and CD8 coreceptors. The DN stage is heterogeneous and can be subdivided into four distinct subsets in mice based on the expression of CD44 and CD25. In human, three distinct DN stages can be recognized: a CD34+CD38−CD1a− stage that represents the most immature thymic subset and the consecutive CD34+CD38+CD1a− and CD34+CD38+CD1a+ stages. Human DN thymocytes mature via an immature single positive (ISP CD4+) and a DP stage into CD4+ or CD8+ SP T cells that express functional T cell receptors (TCR) and that exit the thymus. In this study, gene expression was measured in each of these nine stages.


systematic_name: M6228
exact_source: GSE22601_3409_200_DN
source_species_code: HS
GEO_id: GSE22601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in double negative thymocyte versus immature CD4 [GeneID=920] single positive cells.

description_full:
  T cells develop from progenitors that migrate from the bone marrow into the thymus. Thymocytes are subdivided roughly as being double negative (DN), double positive (DP), or single positive (SP), based on the expression of the CD4 and CD8 coreceptors. The DN stage is heterogeneous and can be subdivided into four distinct subsets in mice based on the expression of CD44 and CD25. In human, three distinct DN stages can be recognized: a CD34+CD38−CD1a− stage that represents the most immature thymic subset and the consecutive CD34+CD38+CD1a− and CD34+CD38+CD1a+ stages. Human DN thymocytes mature via an immature single positive (ISP CD4+) and a DP stage into CD4+ or CD8+ SP T cells that express functional T cell receptors (TCR) and that exit the thymus. In this study, gene expression was measured in each of these nine stages.


systematic_name: M6232
exact_source: GSE22601_3413_200_UP
source_species_code: HS
GEO_id: GSE22601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in immature CD4 [GeneID=920] single positive cells versus double positive thymocytes.

description_full:
[cell repeats an earlier one in this file: 831 characters]


systematic_name: M6234
exact_source: GSE22601_3409_200_UP
source_species_code: HS
GEO_id: GSE22601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in double negative thymocyte versus immature CD4 [GeneID=920] single positive cells.

description_full:
[cell repeats an earlier one in this file: 831 characters]


systematic_name: M6247
exact_source: GSE22601_3413_200_DN
source_species_code: HS
GEO_id: GSE22601
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in immature CD4 [GeneID=920] single positive cells versus double positive thymocytes.

description_full:
[cell repeats an earlier one in this file: 831 characters]


description_brief: Genes up-regulated in T cells: CD4 [GeneID=920] versus CD8.
systematic_name: M6254
exact_source: GSE8835_3369_200_UP
source_species_code: HS
GEO_id: GSE8835
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  To examine the impact of tumors on the immune system, we compared global gene expression profiles of peripheral blood T cells from previously untreated patients with B cell chronic lymphocytic leukemia (CLL) with those from age-matched healthy donors. Although the cells analyzed were not part of the malignant clone, analysis revealed differentially expressed genes, mainly involved in cell differentiation in CD4 cells and defects in cytoskeleton formation, vesicle trafficking, and cytotoxicity in CD8 cells of the CLL patients. In coculture experiments using CLL cells and T cells from healthy allogeneic donors, similar defects developed in both CD4 and CD8 cells. These changes were induced only with direct contact and were not cytokine mediated. Identification of the specific pathways perturbed in the T cells of cancer-bearing patients will allow us to assess steps to repair these defects, which will likely be required to enhance antitumor immunity. Gene expression profiling was performed to determine whether CLL cells induce changes in T cells in patients with CLL.


systematic_name: M6256
exact_source: GSE8835_3370_200_UP
source_species_code: HS
GEO_id: GSE8835
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in T cells from CLL (chronic lymphocytic leukemia) patients: CD4 [GeneID=920] versus CD8.

description_full:
  To examine the impact of tumors on the immune system, we compared global gene expression profiles of peripheral blood T cells from previously untreated patients with B cell chronic lymphocytic leukemia (CLL) with those from age-matched healthy donors. Although the cells analyzed were not part of the malignant clone, analysis revealed differentially expressed genes, mainly involved in cell differentiation in CD4 cells and defects in cytoskeleton formation, vesicle trafficking, and cytotoxicity in CD8 cells of the CLL patients. In coculture experiments using CLL cells and T cells from healthy allogeneic donors, similar defects developed in both CD4 and CD8 cells. These changes were induced only with direct contact and were not cytokine mediated. Identification of the specific pathways perturbed in the T cells of cancer-bearing patients will allow us to assess steps to repair these defects, which will likely be required to enhance antitumor immunity. Gene expression profiling was performed to determine whether CLL cells induce changes in T cells in patients with CLL.


systematic_name: M6258
exact_source: GSE8835_3370_200_DN
source_species_code: HS
GEO_id: GSE8835
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in T cells from CLL (chronic lymphocytic leukemia) patients: CD4 [GeneID=920] versus CD8.

description_full:
[cell repeats an earlier one in this file: 1080 characters]


systematic_name: M6261
exact_source: GSE8835_3371_200_DN
source_species_code: HS
GEO_id: GSE8835
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells: healthy versus CLL (chronic lymphocytic leukemia)l.

description_full:
[cell repeats an earlier one in this file: 1080 characters]


description_brief: Genes down-regulated in cortical thymic epithelial cells (cTEC) versus thymic macrophages.
systematic_name: M6264
exact_source: GSE2585_3567_200_DN
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Gene expression in different thymic stromal cells and subsets thereof was analyzed in 6-12 week old wild type (C57BL/6) and Aire knock-out (mixed background) mice. Thymic stromal cells were purified by sequential enzymatic digestion (collagenase, collagenase/dispase and trypsin) followed by gradient centrifugation and FACS sorting. Sort criteria were as follows: dendritic cells (CD11c+, F4/80 -), macrophages (F4/80+, CD11c-), cTECs (CD45–/lo, CDR1/Ly51+, Ep-CAM+) and mTECs (CD45–/lo, CDR1/Ly51–, Ep-CAM+). mTECs of wild-type and Aire knock-out mice were further subdivided according to CD80 expression levels. For microarray analysis total RNA from thymic stromal cell samples of two independent experiments was pre-amplified and biotinylated by two rounds of cDNA synthesis and in vitro transcription. Fluorescence readings were evaluated by using Microarray Suite 5.0 software.


systematic_name: M6266
exact_source: GSE2585_3564_200_UP
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in medullary thymic epithelial cells (mTEC) with CD80 [GeneID=941] high: AIRE [GeneID=326] knockout versus wildtype.

description_full:
  Gene expression in different thymic stromal cells and subsets thereof was analyzed in 6-12 week old wild type (C57BL/6) and Aire knock-out (mixed background) mice. Thymic stromal cells were purified by sequential enzymatic digestion (collagenase, collagenase/dispase and trypsin) followed by gradient centrifugation and FACS sorting. Sort criteria were as follows: dendritic cells (CD11c+, F4/80 -), macrophages (F4/80+, CD11c-), cTECs (CD45–/lo, CDR1/Ly51+, Ep-CAM+) and mTECs (CD45–/lo, CDR1/Ly51–, Ep-CAM+). mTECs of wild-type and Aire knock-out mice were further subdivided according to CD80 expression levels. For microarray analysis total RNA from thymic stromal cell samples of two independent experiments was pre-amplified and biotinylated by two rounds of cDNA synthesis and in vitro transcription. Fluorescence readings were evaluated by using Microarray Suite 5.0 software.


systematic_name: M6269
exact_source: GSE2585_3562_200_UP
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in medullary thymic epithelial cells (mTEC) with AIRE [GeneID=326] knockout: CD80 [GeneID=941] high versus low.

description_full:
[cell repeats an earlier one in this file: 884 characters]


systematic_name: M6270
exact_source: GSE2585_3565_200_DN
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in medullary thymic epithelial cells (mTEC) with CD80 [GeneID=941] low: AIRE [GeneID=326] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 884 characters]


systematic_name: M6273
exact_source: GSE2585_3564_200_DN
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in medullary thymic epithelial cells (mTEC) with CD80 [GeneID=941] high: AIRE [GeneID=326] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 884 characters]


systematic_name: M6275
exact_source: GSE2585_3562_200_DN
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in medullary thymic epithelial cells (mTEC) with AIRE [GeneID=326] knockout: CD80 [GeneID=941] high versus low.

description_full:
[cell repeats an earlier one in this file: 884 characters]


systematic_name: M6278
exact_source: GSE2585_3565_200_UP
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in medullary thymic epithelial cells (mTEC) with CD80 [GeneID=941] low: AIRE [GeneID=326] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 884 characters]


systematic_name: M6282
exact_source: GSE2585_3563_200_DN
source_species_code: MM
GEO_id: GSE2585
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in medullary thymic epithelial cells (mTEC): CD80 [GeneID=941] high versus low.

description_full:
[cell repeats an earlier one in this file: 884 characters]


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6295
exact_source: GSE1925_3036_200_UP
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages primed by IFNG [GeneID=3458]: untreated versus stimulated by IFNG [GeneID=3458] for 3h.


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6296
exact_source: GSE1925_3039_200_UP
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages stimulated by IFNG [GeneID=3458] for 3h: control versus primed by IFNG [GeneID=3458].


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6297
exact_source: GSE1925_3039_200_DN
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages stimulated by IFNG [GeneID=3458] for 3h: control versus primed by IFNG [GeneID=3458].


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6299
exact_source: GSE1925_3037_200_DN
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages primed by IFNG [GeneID=3458]: untreated versus stimulated by IFNG [GeneID=3458] for 24h.


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6301
exact_source: GSE1925_3038_200_DN
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages primed and then stimulated by IFNG [GeneID=3458]: 3h versus 24h.


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6307
exact_source: GSE1925_3040_200_UP
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages stimulated by IFNG [GeneID=3458] for 24h: control versus primed by IFNG [GeneID=3458].


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6309
exact_source: GSE1925_3040_200_DN
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages stimulated by IFNG [GeneID=3458] for 24h: control versus primed by IFNG [GeneID=3458].


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6310
exact_source: GSE1925_3036_200_DN
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in macrophages primed by IFNG [GeneID=3458]: untreated versus stimulated by IFNG [GeneID=3458] for 3h.


description_full: IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
systematic_name: M6314
exact_source: GSE1925_3037_200_UP
source_species_code: HS
GEO_id: GSE1925
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in macrophages primed by IFNG [GeneID=3458]: untreated versus stimulated by IFNG [GeneID=3458] for 24h.


description_brief: Genes up-regulated in macrophages: control versus Sendai virus infection.
systematic_name: M6316
exact_source: GSE2935_2664_200_UP
source_species_code: MM
GEO_id: GSE2935
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Thus, mouse macrophage cultures were established from PBMCs isolated from wild-type control mice and were inoculated with SeV (Sendai virus) or UV-SeV (UV-inactivated SeV). These microarrays were performed in concert with assays of CCL5 and CCR5 expression, viral replication, and cellular apoptosis. Initial experiments indicated that wild-type mouse macrophages inoculated with SeV exhibit induction of CCL5 mRNA to the highest level of any known mouse gene product, while mRNA levels for CCL5 receptors (CCR5 as well as CCR3 and CCR1) or alternative ligands for these receptors (CCL3 and CCL4) were relatively unchanged by viral infection.


description_brief: Genes down-regulated in spleen from DUSP1 [GeneID=1843] knockout: control versus LPS.
systematic_name: M6321
exact_source: GSE3565_2621_200_DN
source_species_code: MM
GEO_id: GSE3565
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Activation of the Mitogen activated protein kinase (MAPK) cascade following Toll-like receptor (TLR) stimulation enables innate immune cells to rapidly activate cytokine gene expression. A balanced response to signals of infectious danger requires that cellular activation is transient. Here, we identify the MAPK phosphatase Dual specificity phosphatase-1 (DUSP1) as an essential endogenous regulator of the inflammatory response to LPS. DUSP1-deficient (DUSP1-/-) bone marrow derived macrophages showed selectively prolonged activation of p38 MAPK and increased cytokine production. Intraperitoneal challenge of DUSP1-/- mice with LPS caused increased lethality and overshooting production of IL-6 and TNF-alpha. Transcriptional profiling revealed that DUSP1 controls a significant fraction of LPS-induced genes, that includes IL-6 and IL-10 as well as the chemokines CCL3, CCL4 and CXCL2. In contrast, the expression of the important mediators of endotoxin lethality, IFN-gamma and IL-12, was not significantly altered by the absence of DUSP1. These data together demonstrate a specific regulatory role of DUSP1 in controlling a subset of LPS-induced genes that determines the outcome of endotoxin shock.


systematic_name: M6332
exact_source: GSE3565_2624_200_UP
source_species_code: MM
GEO_id: GSE3565
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleen from mice injected with LPS: DUSP1 [GeneID=1843] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1207 characters]


systematic_name: M6333
exact_source: GSE3565_2624_200_DN
source_species_code: MM
GEO_id: GSE3565
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen from mice injected with LPS: DUSP1 [GeneID=1843] knockout versus wildtype.

description_full:
[cell repeats an earlier one in this file: 1207 characters]


description_brief: Genes up-regulated in Vd2 gamma delta T cells: untreated versus LPS.
systematic_name: M6337
exact_source: GSE3720_3346_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The two major human gd T cell subsets, Vd1 and Vd2, display differences in tissue tropism and agonist responses, but we have little insight into global differences that may exist at the gene expression level. This is due to the small numbers of these cells that can be obtained from healthy donors, which limit comprehensive, comparative gene expression analyses. We established a culture method that expands Vd1 and Vd2 cells from the same PBL preparation to levels sufficient for sorting and microarray analysis. Although the subsets were expanded identically (anti-TCR mAb, plus IL-15), 392 and 614 genes were identified, which were differentially expressed in the two subsets, from two donors, respectively. Approximately 4,500 genes changed in both subsets following PMA/ionomycin treatment; about 50% of these genes were subset-specific. Both subsets responded to a crude LPS preparation, but only 6% of the responsive genes were the same. The differentially expressed genes were consistent with Vd2 cells being more inflammatory and Vd1 cells having more of a regulatory phenotype. Both subsets expressed transcripts encoding an array of innate and NK cell receptors, supporting the relationship of gd T cells to the innate immune system. Our results show that circulating Vd1 and Vd2 subsets in humans have considerable, inherent differences in gene expression following treatment with non-TCR agonists, supporting unique functional roles for these cells in vivo.


systematic_name: M6340
exact_source: GSE3720_3347_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in Vd2 gamma delta T cells: untreated versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
  The two major human gd T cell subsets, Vd1 and Vd2, display differences in tissue tropism and agonist responses, but we have little insight into global differences that may exist at the gene expression level. This is due to the small numbers of these cells that can be obtained from healthy donors, which limit comprehensive, comparative gene expression analyses. We established a culture method that expands Vd1 and Vd2 cells from the same PBL preparation to levels sufficient for sorting and microarray analysis. Although the subsets were expanded identically (anti-TCR mAb, plus IL-15), 392 and 614 genes were identified, which were differentially expressed in the two subsets, from two donors, respectively. Approximately 4,500 genes changed in both subsets following PMA/ionomycin treatment; about 50% of these genes were subset-specific. Both subsets responded to a crude LPS preparation, but only 6% of the responsive genes were the same. The differentially expressed genes were consistent with Vd2 cells being more inflammatory and Vd1 cells having more of a regulatory phenotype. Both subsets expressed transcripts encoding an array of innate and NK cell receptors, supporting the relationship of gd T cells to the innate immune system. Our results show that circulating Vd1 and Vd2 subsets in humans have considerable, inherent differences in gene expression following treatment with non-TCR agonists, supporting unique functional roles for these cells in vivo.


systematic_name: M6343
exact_source: GSE3720_3344_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in Vd1 gamma delta T cells: untreated versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6344
exact_source: GSE3720_3344_200_DN
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Vd1 gamma delta T cells: untreated versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6345
exact_source: GSE3720_3345_200_DN
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Vd1 gamma delta T cells: LPS versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6346
exact_source: GSE3720_3348_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in Vd2 gamma delta T cells: LPS versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6347
exact_source: GSE3720_3348_200_DN
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Vd2 gamma delta T cells: LPS versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6348
exact_source: GSE3720_3345_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in Vd1 gamma delta T cells: LPS versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6351
exact_source: GSE3720_3347_200_DN
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in Vd2 gamma delta T cells: untreated versus phorbol myristate acetate and ionomycin [PubChem=4792;3733].

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6356
exact_source: GSE3720_3351_200_UP
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in gamma delta T cells stimulated by phorbol myristate acetate and ionomycin [PubChem=4792;3733]: Vd1 versus Vd2.

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6360
exact_source: GSE3720_3351_200_DN
source_species_code: HS
GEO_id: GSE3720
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in gamma delta T cells stimulated by phorbol myristate acetate and ionomycin [PubChem=4792;3733]: Vd1 versus Vd2.

description_full:
[cell repeats an earlier one in this file: 1471 characters]


systematic_name: M6363
exact_source: GSE3691_2655_200_UP
source_species_code: MM
GEO_id: GSE3691
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendiritic cells from speen: interferon producing killer cells versus conventional.

description_full:
  To characterize differences between BALB/c splenic CD11cintB220+Gr1+ PDCs (plasmacytoid dendritic cells), CD11cintB220+CD49b+ IKDCs (interferon producing killer-dendritic cells), and CD11chighB220- cDCs (conventional dendritic cells), we performed gene expression profile analysis using Affymetrix chips. We FACS-sorted BALB/c spleen DC subpopulations. Comparison of differentially expressed genes between IKDCs and cDCs vividly revealed selective expression of multiple NK-related genes in IKDCs . These included granzymes A, B, K and M, perforin, Fas ligand, and NK receptors such as NKG2A, NKG2D, Ly49 family genes, NKR-P1, NKG7, NKp46 and Mafa (KLRG1). No NK-related genes were highly expressed in the PDCs.


systematic_name: M6365
exact_source: GSE3691_2656_200_DN
source_species_code: MM
GEO_id: GSE3691
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendiritic cells from speen: interferon producing killer cells versus plasmacytoid.

description_full:
  To characterize differences between BALB/c splenic CD11cintB220+Gr1+ PDCs (plasmacytoid dendritic cells), CD11cintB220+CD49b+ IKDCs (interferon producing killer-dendritic cells), and CD11chighB220- cDCs (conventional dendritic cells), we performed gene expression profile analysis using Affymetrix chips. We FACS-sorted BALB/c spleen DC subpopulations. Comparison of differentially expressed genes between IKDCs and cDCs vividly revealed selective expression of multiple NK-related genes in IKDCs . These included granzymes A, B, K and M, perforin, Fas ligand, and NK receptors such as NKG2A, NKG2D, Ly49 family genes, NKR-P1, NKG7, NKp46 and Mafa (KLRG1). No NK-related genes were highly expressed in the PDCs.


systematic_name: M6366
exact_source: GSE3691_2655_200_DN
source_species_code: MM
GEO_id: GSE3691
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendiritic cells from speen: interferon producing killer cells versus conventional.

description_full:
  To characterize differences between BALB/c splenic CD11cintB220+Gr1+ PDCs (plasmacytoid dendritic cells), CD11cintB220+CD49b+ IKDCs (interferon producing killer-dendritic cells), and CD11chighB220- cDCs (conventional dendritic cells), we performed gene expression profile analysis using Affymetrix chips. We FACS-sorted BALB/c spleen DC subpopulations. Comparison of differentially expressed genes between IKDCs and cDCs vividly revealed selective expression of multiple NK-related genes in IKDCs . These included granzymes A, B, K and M, perforin, Fas ligand, and NK receptors such as NKG2A, NKG2D, Ly49 family genes, NKR-P1, NKG7, NKp46 and Mafa (KLRG1). No NK-related genes were highly expressed in the PDCs.


systematic_name: M6367
exact_source: GSE3691_2656_200_UP
source_species_code: MM
GEO_id: GSE3691
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendiritic cells from speen: interferon producing killer cells versus plasmacytoid.

description_full:
[cell repeats an earlier one in this file: 711 characters]


systematic_name: M6371
exact_source: GSE3994_2711_200_UP
source_species_code: MM
GEO_id: GSE3994
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived mast cells: wildtype versus ADCYAP1R1 [GeneID=117] knockout.

description_full:
  Bone marrow-derived mast cells were differentiated over 4-6 weeks using bone marrow from Pac-1+/+ and Pac1-/- littermate mice. Cell purity was 99% c-kit and Fc epsilon receptor positive as assessed by flow cytometry. Cells were stimulated by Fc epsilon receptor crosslinking using IgE-DNP/HSA for sensitization for 18 hours and DNP-HSA antigen for crosslinking for 2 hours. Gene transcript abundance was determined and scaled to 150 using alogorithms in MicroArray Analysis Suite Software 5.0 (Affymetrix).


systematic_name: M6372
exact_source: GSE3994_2711_200_DN
source_species_code: MM
GEO_id: GSE3994
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived mast cells: wildtype versus ADCYAP1R1 [GeneID=117] knockout.

description_full:
  Bone marrow-derived mast cells were differentiated over 4-6 weeks using bone marrow from Pac-1+/+ and Pac1-/- littermate mice. Cell purity was 99% c-kit and Fc epsilon receptor positive as assessed by flow cytometry. Cells were stimulated by Fc epsilon receptor crosslinking using IgE-DNP/HSA for sensitization for 18 hours and DNP-HSA antigen for crosslinking for 2 hours. Gene transcript abundance was determined and scaled to 150 using alogorithms in MicroArray Analysis Suite Software 5.0 (Affymetrix).


description_brief: Genes down-regulated in naïve B lymphocytes versus plasma cells.
systematic_name: M6374
exact_source: GSE4142_3222_200_DN
source_species_code: MM
GEO_id: GSE4142
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  In order to better understand the factors that regulate B cell differentiation upon exposure to antigen, we compares global gene expression profiles from naive B cells with antigen-specific plasma, germinal center, and memory B cells after immunization with the T-dependent antigen, NP-CGG. The memory B cell-enriched transcripts were then compared with memory T cell-enriched and hematopoietic stem cell-enriched transcripts in order to generate a transcriptional profile of self-renewal within the hematopoietic system.


description_brief: Genes up-regulated in monocytes: untreated versus M. tuberculosis 19 kDa lipopeptide (3h).
systematic_name: M6398
exact_source: GSE8921_3121_200_UP
source_species_code: HS
GEO_id: GSE8921
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  In innate immune responses, activation of Toll-like receptors (TLRs) triggers direct antimicrobial activity against intracellular bacteria, which in murine, but not human, monocytes and macrophages is mediated principally by nitric oxide. We report here that TLR activation of human macrophages up-regulated expression of the vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to induction of the antimicrobial peptide cathelicidin and killing of intracellular Mycobacterium tuberculosis. We also observed that sera from African-American individuals, known to have increased susceptibility to tuberculosis, had low 25-hydroxyvitamin D and were inefficient in supporting cathelicidin messenger RNA induction. These data support a link between TLRs and vitamin D-mediated innate immunity and suggest that differences in ability of human populations to produce vitamin D may contribute to susceptibility to microbial infection.


description_brief: Genes up-regulated in CD4 [GeneID=920] T cells versus NKT cells.
systematic_name: M6426
exact_source: GSE3039_3200_200_UP
source_species_code: MM
GEO_id: GSE3039
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Three innate (B1-B, NKT, CD8aaT cells) and adaptive (B2-B, CD4T, CD8abT cells) cell-types were sorted by FACS. Three biological replicates for NKT, CD4T, CD8aaT, CD8abT cells and two biological replicates for B1 and B2 cells were generated and the expression profiles were determined using Affymetrix Mu74Av2 chip. Comparisons between the sample groups allow the identification of genes differentially expressed between the innate and adaptive cell-types.


systematic_name: M6477
exact_source: GSE4748_3382_200_UP
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: untreated versus LPS like antigen from O. planktothrix (3h).

description_full:
  A cyanobacterial LPS antagonist prevents endotoxin shock and blocks sustained TLR4 stimulation required for cytokine expression. We report the identification and biologic characterization of an LPS-like molecule extracted from the cyanobacterium Oscillatoria Planktothrix FP1 (CyP).


systematic_name: M6478
exact_source: GSE4748_3382_200_DN
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: untreated versus LPS like antigen from O. planktothrix (3h).

description_full:
  A cyanobacterial LPS antagonist prevents endotoxin shock and blocks sustained TLR4 stimulation required for cytokine expression. We report the identification and biologic characterization of an LPS-like molecule extracted from the cyanobacterium Oscillatoria Planktothrix FP1 (CyP).


systematic_name: M6484
exact_source: GSE4748_3384_200_UP
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: untreated versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6485
exact_source: GSE4748_3384_200_DN
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: untreated versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6486
exact_source: GSE4748_3385_200_UP
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: untreated versus LPS like antigen from O. planktothrix (1h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6488
exact_source: GSE4748_3385_200_DN
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: untreated versus LPS like antigen from O. planktothrix (1h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6491
exact_source: GSE4748_3386_200_UP
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: LPS like antigen from O. planktothrix (3h) versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6492
exact_source: GSE4748_3386_200_DN
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: LPS like antigen from O. planktothrix (3h) versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6493
exact_source: GSE4748_3387_200_UP
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: LPS (3h) versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


systematic_name: M6494
exact_source: GSE4748_3387_200_DN
source_species_code: HS
GEO_id: GSE4748
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: LPS (3h) versus LPS and LPS like antigen from O. planktothrix (3h).

description_full:
[cell repeats an earlier one in this file: 282 characters]


description_full: Human monocyte derived dendritic cells matured via galectin-1 or LPS.
systematic_name: M6495
exact_source: GSE4984_2744_200_UP
source_species_code: HS
GEO_id: GSE4984
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: control versus treated with LGALS1 [GeneID=3956].


description_full: Human monocyte derived dendritic cells matured via galectin-1 or LPS.
systematic_name: M6496
exact_source: GSE4984_2744_200_DN
source_species_code: HS
GEO_id: GSE4984
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: control versus treated with LGALS1 [GeneID=3956].


description_brief: Genes up-regulated in epithelial cells (6h): untreated versus IFNG [GeneID=3458].
systematic_name: M6512
exact_source: GSE5542_3329_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Type I and type II interferons (IFNs) bind to different cell surface receptors but activate overlapping signal transduction pathways. We examined the effects of a type I IFN (IFN-acon1) and a type II iFN (IFN-g1b) on gene experession in A549 cells and demonstrate that there is a common set of genes modulated by both IFNs as well as a set of gene specifically regulated by each, reflecting the activation of different signaling pathways. In particualr, IFN-g induced many more genes of the signaling pathways, apoptosis, and cytokine interactions than did IFN-a. Even with genes induced by both IFNs there were distinctive quantitativive differences in expression. IFN-g1b plays a major role in the induction and regulation of the complement pathway. Previous work has shown a synergistic antivral and antiproliferative effect of type I and type II IFNs in cell culture and in the treament of tumors in mice. We demonstrate that a majority of genes showed and additive effect of IFN-acon1 and IFN-g1b, but a subset of gene is synergistically induced; these incluce ISG10, MX2, OAS2, and other genes known to be involved in the antiviral response, TRAIL (TNFSF10) and caspases involved in apoptosis and chemokine genes RANTES, CXCL10, and CXCL11. Greater than additive transcription of some of these genes in the presence of both IFNs was confirmed by real-time kinetic RT-PCR. Elevated induction of many of these genes may be sufficient to explain the synergistic antiviral and antitumor effects of this combination of IFNS in vivo.


systematic_name: M6518
exact_source: GSE5542_3331_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (6h): untreated versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6519
exact_source: GSE5542_3331_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (6h): untreated versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6527
exact_source: GSE5542_3334_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (24h): untreated versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6529
exact_source: GSE5542_3334_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (24h): untreated versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6531
exact_source: GSE5542_3335_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (6h): IFNG [GeneID=3458] versus IFNG [GeneID=3458] and interferon alpha.

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6533
exact_source: GSE5542_3335_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (6h): IFNG [GeneID=3458] versus IFNG [GeneID=3458] and interferon alpha.

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6535
exact_source: GSE5542_3336_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (24h): IFNG [GeneID=3458] versus IFNG [GeneID=3458] and interferon alpha.

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6536
exact_source: GSE5542_3336_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (24h): IFNG [GeneID=3458] versus IFNG [GeneID=3458] and interferon alpha.

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6537
exact_source: GSE5542_3337_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (6h): interferon alpha versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6538
exact_source: GSE5542_3337_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (6h): interferon alpha versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6539
exact_source: GSE5542_3338_200_UP
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in epithelial cells (24h): interferon alpha versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


systematic_name: M6540
exact_source: GSE5542_3338_200_DN
source_species_code: HS
GEO_id: GSE5542
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in epithelial cells (24h): interferon alpha versus interferon alpha and IFNG [GeneID=3458].

description_full:
[cell repeats an earlier one in this file: 1533 characters]


description_brief: Genes up-regulated in activated macrophages: classically (M1) versus alternative (M2).
systematic_name: M6547
exact_source: GSE4811_3341_200_UP
source_species_code: MM
GEO_id: GSE4811
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The purpose of this study is to identify novel markers for the type II activated macrophage, which is generated by classical stimulation in the presence if IgG immune complexes. These cells gererally produce high levels of IL-10 and low levels of IL-12, in comparison to classically activated macrophages. We wish to identify gene expression which is enriched in Type II activated macrophages in comparison to classically activated macrophages.


description_brief: Genes up-regulated in CD8 T cells: control versus over-expressing TERT [GeneID=7015].
systematic_name: M6549
exact_source: GSE5142_3572_200_UP
source_species_code: HS
GEO_id: GSE5142
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Using CD8+ T lymphocyte clones over-expressing telomerase weinvestigated the molecular mechanisms that regulate T cell proliferation. Transduction and subcloning procedures were performed on CD8 + naive T-cell clones isolated from two different healthy individuals aged between 30 to 35 years (HD1 and HD2). T-cell cloneswere transduced to express hTERT/GFP or GFP alone. HD2 was profiled on U133Plus 2.0 and submitted as a separate GEO series.


systematic_name: M6551
exact_source: GSE5142_3573_200_UP
source_species_code: HS
GEO_id: GSE5142
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD8 T cells: early passage clone over-expressing TERT [GeneID=7015] versus late passage control.

description_full:
  Using CD8+ T lymphocyte clones over-expressing telomerase weinvestigated the molecular mechanisms that regulate T cell proliferation. Transduction and subcloning procedures were performed on CD8 + naive T-cell clones isolated from two different healthy individuals aged between 30 to 35 years (HD1 and HD2). T-cell cloneswere transduced to express hTERT/GFP or GFP alone. HD2 was profiled on U133Plus 2.0 and submitted as a separate GEO series.


systematic_name: M6552
exact_source: GSE5142_3573_200_DN
source_species_code: HS
GEO_id: GSE5142
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD8 T cells: early passage clone over-expressing TERT [GeneID=7015] versus late passage control.

description_full:
[cell repeats an earlier one in this file: 444 characters]


systematic_name: M6553
exact_source: GSE5679_3388_200_UP
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: untreated versus rosiglitazone [PubChem=77999].

description_full:
  Our data indicated that activation of the PPARg nuclear receptor induces a retinoid response in human dendritic cells. In order to assess the contribution of retinoid signaling to the PPARg response we decided to use a combination of pharmacological activators and inhibitors of these pathways. Cells were treated with the synthetic PPARg ligand rosiglitazone (RSG), or with RSG along with the RARa antagonist (AGN193109) to block RARa mediated gene expression, or the RARa specific agonists (AM580) alone. This design allows one to determine if retinoid signaling is a downstream event of PPARg activation and what portion of PPARg regulated genes are regulated via induced retinoid signaling.


systematic_name: M6554
exact_source: GSE5679_3388_200_DN
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: untreated versus rosiglitazone [PubChem=77999].

description_full:
  Our data indicated that activation of the PPARg nuclear receptor induces a retinoid response in human dendritic cells. In order to assess the contribution of retinoid signaling to the PPARg response we decided to use a combination of pharmacological activators and inhibitors of these pathways. Cells were treated with the synthetic PPARg ligand rosiglitazone (RSG), or with RSG along with the RARa antagonist (AGN193109) to block RARa mediated gene expression, or the RARa specific agonists (AM580) alone. This design allows one to determine if retinoid signaling is a downstream event of PPARg activation and what portion of PPARg regulated genes are regulated via induced retinoid signaling.


systematic_name: M6558
exact_source: GSE5679_3390_200_UP
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: untreated versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6560
exact_source: GSE5679_3390_200_DN
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: untreated versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6561
exact_source: GSE5679_3391_200_UP
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: rosiglitazone [PubChem=77999] versus AM580 [PubChem=2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6563
exact_source: GSE5679_3391_200_DN
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: rosiglitazone [PubChem=77999] versus AM580 [PubChem=2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6565
exact_source: GSE5679_3392_200_UP
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: rosiglitazone [PubChem=77999] versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6567
exact_source: GSE5679_3392_200_DN
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: rosiglitazone [PubChem=77999] versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6569
exact_source: GSE5679_3393_200_UP
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in monocyte-derived dendritic cells: AM580 [PubChem=2126] versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


systematic_name: M6570
exact_source: GSE5679_3393_200_DN
source_species_code: HS
GEO_id: GSE5679
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in monocyte-derived dendritic cells: AM580 [PubChem=2126] versus rosiglitazone and AM580 [PubChem=77999;2126].

description_full:
[cell repeats an earlier one in this file: 694 characters]


description_brief: Genes up-regulated in ITGAM+ [GeneID=3684] cells from spleen: healthy versus tumor bearing mice.
systematic_name: M6575
exact_source: GSE5455_2445_200_UP
source_species_code: MM
GEO_id: GSE5455
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Active suppression of tumor-specific T lymphocytes can limit the immune-surveillance and immunotherapy efficacy. While tumor-recruited CD11b+ myeloid cells are known mediators of tumor-associated immune dysfunction, the true nature of these suppressive cells and the fine biochemical pathways governing their immunosuppressive activity remain elusive. Here we describe a population of circulating CD11b+/IL-4Rα+, inflammatory-type monocytes that is elicited by growing tumors and activated by IFN-γ released from T lymphocytes. CD11b+/IL-4Rα+ cells produce IL-13 and IFN-γ and integrate the downstream signals of these cytokines to trigger the molecular pathways suppressing antigen-activated CD8+ T lymphocytes. Analogous immunosuppressive circuits are active in CD11b+ cells present within the tumor microenvironment. These suppressor cells challenge the current idea that tumor-conditioned immunosuppressive monocytes/macrophages are alternatively activated. Moreover, our data show how the inflammatory response elicited by tumors has detrimental effects on the adaptive immune system and suggest novel approaches for the treatment of tumorinduced immune dysfunctions.


systematic_name: M6577
exact_source: GSE5455_2446_200_UP
source_species_code: MM
GEO_id: GSE5455
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ITGAM+ [GeneID=3684] cells (incubated for 24h in complete medium) from spleen: healthy versus tumor bearing mice.

description_full:
  Active suppression of tumor-specific T lymphocytes can limit the immune-surveillance and immunotherapy efficacy. While tumor-recruited CD11b+ myeloid cells are known mediators of tumor-associated immune dysfunction, the true nature of these suppressive cells and the fine biochemical pathways governing their immunosuppressive activity remain elusive. Here we describe a population of circulating CD11b+/IL-4Rα+, inflammatory-type monocytes that is elicited by growing tumors and activated by IFN-γ released from T lymphocytes. CD11b+/IL-4Rα+ cells produce IL-13 and IFN-γ and integrate the downstream signals of these cytokines to trigger the molecular pathways suppressing antigen-activated CD8+ T lymphocytes. Analogous immunosuppressive circuits are active in CD11b+ cells present within the tumor microenvironment. These suppressor cells challenge the current idea that tumor-conditioned immunosuppressive monocytes/macrophages are alternatively activated. Moreover, our data show how the inflammatory response elicited by tumors has detrimental effects on the adaptive immune system and suggest novel approaches for the treatment of tumorinduced immune dysfunctions.


systematic_name: M6578
exact_source: GSE5455_2446_200_DN
source_species_code: MM
GEO_id: GSE5455
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ITGAM+ [GeneID=3684] cells (incubated for 24h in complete medium) from spleen: healthy versus tumor bearing mice.

description_full:
[cell repeats an earlier one in this file: 1172 characters]


systematic_name: M6579
exact_source: GSE5455_2447_200_UP
source_species_code: MM
GEO_id: GSE5455
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in ITGAM+ [GeneID=3684] cells from spleens of tumor bearing mice: processed immediately versus those incubated for 24h in complete medium.

description_full:
[cell repeats an earlier one in this file: 1172 characters]


systematic_name: M6580
exact_source: GSE5455_2447_200_DN
source_species_code: MM
GEO_id: GSE5455
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in ITGAM+ [GeneID=3684] cells from spleens of tumor bearing mice: processed immediately versus those incubated for 24h in complete medium.

description_full:
[cell repeats an earlier one in this file: 1172 characters]


description_brief: Genes up-regulated in monocytes: untreated versus CSF1 [GeneID=1435].
systematic_name: M6581
exact_source: GSE5099_3803_200_UP
source_species_code: HS
GEO_id: GSE5099
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Monocytes mature tom acrophages in the presence of the lineage determining cytokine M-CSF. They can be further polarized into M1 or M2 macrophages with distinct functional properties. We used microarrays to detail the global programme of gene expression underlying macrophage maturation and polarization and identified distinct classes of up-regulated genes during this process.


systematic_name: M6584
exact_source: GSE5099_3804_200_UP
source_species_code: HS
GEO_id: GSE5099
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in unstimulated monocytes versus macrophages incubated with CSF1 [GeneID=435] at day 7.

description_full:
  Monocytes mature tom acrophages in the presence of the lineage determining cytokine M-CSF. They can be further polarized into M1 or M2 macrophages with distinct functional properties. We used microarrays to detail the global programme of gene expression underlying macrophage maturation and polarization and identified distinct classes of up-regulated genes during this process.


systematic_name: M6585
exact_source: GSE5099_3804_200_DN
source_species_code: HS
GEO_id: GSE5099
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in unstimulated monocytes versus macrophages incubated with CSF1 [GeneID=435] at day 7.

description_full:
[cell repeats an earlier one in this file: 378 characters]


systematic_name: M6592
exact_source: GSE5099_3807_200_UP
source_species_code: HS
GEO_id: GSE5099
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated upon CSF1 [GeneID=1435] treatment: monocytes (3 days) versus macrophages (7 days).

description_full:
[cell repeats an earlier one in this file: 378 characters]


systematic_name: M6593
exact_source: GSE5099_3807_200_DN
source_species_code: HS
GEO_id: GSE5099
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated upon CSF1 [GeneID=1435] treatment: monocytes (3 days) versus macrophages (7 days).

description_full:
[cell repeats an earlier one in this file: 378 characters]


description_brief: Genes up-regulated in bone marrow-derived macrophages: untreated (0 min) versus LPS (45 min).
systematic_name: M6597
exact_source: GSE5589_2990_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  IL-10 or IL-6 stimulation of control 129xC57BL/6 murine bone marrow derived macrophages in the presence of LPS. We used microarrays to detail the global programme of gene expression changes in response to IL-6 or IL-10 stimulation in the presence of lipopolysaccharide. BMDMs were isolated from control, IL-6-/-, and IL-10-/- mice on a 129XBL/6 mixed background mice and differentiated in the presence of CSF-1 for 6-7 days. Cells were scraped and plated in 6 well plates at 2x10e6/well. Cells were washed with complete DMEM and rested for 1-2 hr before stimulation with combinations of IL-10 (10 ng/ml), IL-6 (2 ng/ml) or LPS (100 ng/ml) for 45 min or 180 mins. Complete biological replicates were performed.


systematic_name: M6602
exact_source: GSE5589_2992_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL10 [GeneID=3586] and LPS (45 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6603
exact_source: GSE5589_2992_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL10 [GeneID=3586] and LPS (45 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6604
exact_source: GSE5589_2993_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL10 [GeneID=3586] and LPS (180 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6605
exact_source: GSE5589_2993_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL10 [GeneID=3586] and LPS (180 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6606
exact_source: GSE5589_2994_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL6 [GeneID=3569] and LPS (45 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6607
exact_source: GSE5589_2994_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages: untreated (0 min) versus IL6 [GeneID=3569] and LPS (45 min).

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6609
exact_source: GSE5589_2996_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophage (45 min): LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6610
exact_source: GSE5589_2996_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophage (45 min): LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6611
exact_source: GSE5589_2997_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophage (45 min): LPS versus IL6 [GeneID=3569] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6612
exact_source: GSE5589_2997_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophage (45 min): LPS versus IL6 [GeneID=3569] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6613
exact_source: GSE5589_2998_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages (45 min): IL10 [GeneID=3486] and LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6614
exact_source: GSE5589_2998_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages (45 min): IL10 [GeneID=3486] and LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6615
exact_source: GSE5589_2999_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophage (180 min): LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6617
exact_source: GSE5589_2999_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophage (180 min): LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6618
exact_source: GSE5589_3000_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 45 min of stimulation by: LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6619
exact_source: GSE5589_3000_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 45 min of stimulation by: LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6620
exact_source: GSE5589_3001_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 45 min of stimulation by: LPS versus IL6 [GeneID=3569] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6621
exact_source: GSE5589_3001_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 45 min of stimulation by: LPS versus IL6 [GeneID=3569] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6623
exact_source: GSE5589_3002_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 180 min of stimulation by: LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6624
exact_source: GSE5589_3002_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL6 [GeneID=3569] knockout and 180 min of stimulation by: LPS versus IL10 [GeneID=3586] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6625
exact_source: GSE5589_3003_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL6 [GeneID=3469] knockout and 45 min of stimulation by AIL10 [GeneID=3486] and LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6626
exact_source: GSE5589_3003_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL6 [GeneID=3469] knockout and 45 min of stimulation by AIL10 [GeneID=3486] and LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6629
exact_source: GSE5589_3004_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min of stimulation by: LPS versus LPS and IL10 [GeneID=3486].

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6630
exact_source: GSE5589_3004_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min of stimulation by: LPS versus LPS and IL10 [GeneID=3486].

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6631
exact_source: GSE5589_3005_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min stimulation by: LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6632
exact_source: GSE5589_3005_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min stimulation by: LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6633
exact_source: GSE5589_3006_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] and 180 min stimulation of: LPS versus IL10 [GeneID=3486] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6634
exact_source: GSE5589_3006_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] and 180 min stimulation of: LPS versus IL10 [GeneID=3486] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6635
exact_source: GSE5589_3007_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min of stimulation by: LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6636
exact_source: GSE5589_3007_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages with IL10 [GeneID=3486] knockout and 45 min of stimulation by: LPS versus IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6638
exact_source: GSE5589_3008_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min stimulation by LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6639
exact_source: GSE5589_3008_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min stimulation by LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6640
exact_source: GSE5589_3009_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophagesat 45 min stimulation of IL10 [GeneID=3486] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6644
exact_source: GSE5589_3009_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophagesat 45 min stimulation of IL10 [GeneID=3486] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6645
exact_source: GSE5589_3010_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL6 [GeneID=3469] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6646
exact_source: GSE5589_3010_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL6 [GeneID=3469] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6647
exact_source: GSE5589_3011_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by LPS: wildtype versus IL10 [GeneID=3486].

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6648
exact_source: GSE5589_3011_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by LPS: wildtype versus IL10 [GeneID=3486].

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6649
exact_source: GSE5589_3012_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL10 [GeneID=3486] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6650
exact_source: GSE5589_3012_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL10 [GeneID=3486] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6651
exact_source: GSE5589_3013_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL6 [GeneID=3469] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6652
exact_source: GSE5589_3013_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL6 [GeneID=3469] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6653
exact_source: GSE5589_3014_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6654
exact_source: GSE5589_3014_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6655
exact_source: GSE5589_3015_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL10 [GeneID=3486] and LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6660
exact_source: GSE5589_3015_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 45 min of stimulation by IL10 [GeneID=3486] and LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6661
exact_source: GSE5589_3016_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages (45 min): IL6 [GeneID=3469] knockout stimulated by IL6 [GeneID=3469] and LPS versus IL10 [GeneID=3486] knockout stimulated by and IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6662
exact_source: GSE5589_3016_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages (45 min): IL6 [GeneID=3469] knockout stimulated by IL6 [GeneID=3469] and LPS versus IL10 [GeneID=3486] knockout stimulated by and IL6 [GeneID=3469] and LPS.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6664
exact_source: GSE5589_3017_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophagesat 180 min stimulation by LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6667
exact_source: GSE5589_3017_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophagesat 180 min stimulation by LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6668
exact_source: GSE5589_3018_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophagesat 180 min of stimulation by IL10 [GeneID=3486] and LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6671
exact_source: GSE5589_3018_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophagesat 180 min of stimulation by IL10 [GeneID=3486] and LPS: IL6 [GeneID=3469] knockout versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6673
exact_source: GSE5589_3019_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 180 min of stimulation by LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6675
exact_source: GSE5589_3019_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 180 min of stimulation by LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6676
exact_source: GSE5589_3020_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 180 min of stimulation with IL10 [GeneID=3486] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6677
exact_source: GSE5589_3020_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 180 min of stimulation with IL10 [GeneID=3486] and LPS: wildtype versus IL10 [GeneID=3486] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6678
exact_source: GSE5589_3021_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 180 min of stimulation byLPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6680
exact_source: GSE5589_3021_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 180 min of stimulation byLPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6681
exact_source: GSE5589_3022_200_UP
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in bone marrow-derived macrophages at 180 min of stimulation with IL10 [GeneID=3486] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


systematic_name: M6683
exact_source: GSE5589_3022_200_DN
source_species_code: MM
GEO_id: GSE5589
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in bone marrow-derived macrophages at 180 min of stimulation with IL10 [GeneID=3486] and LPS: wildtype versus IL6 [GeneID=3469] knockout.

description_full:
[cell repeats an earlier one in this file: 709 characters]


description_brief: Genes up-regulated in ndothelial cells: untreated versus interferon alpha.
systematic_name: M6684
exact_source: GSE3920_3481_200_UP
source_species_code: HS
GEO_id: GSE3920
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  IFNs are highly pleiotropic cytokines also endowed with marked anti-angiogenic activity. In this study, the mRNA expression profiles of endothelial cells (EC) exposed in vitro to IFN-alpha, IFN-beta, or IFN-gamma were determined. We found that in HUVEC as well as in other EC types 175 genes were upregulated (>2-fold increase) by IFNs, including genes involved in the host response to RNA viruses, inflammation, and apoptosis. Interestingly, 41 genes showed a >5-fold higher induction by IFN-alpha in EC compared to human fibroblasts; among them, the gene encoding the angiostatic chemokine CXCL11 was selectively induced by IFN-alpha in EC along with other genes associated with angiogenesis regulation, including CXCL10, TRAIL, and guanylate binding protein 1 (GBP-1). These transcriptional changes were confirmed and extended by quantitative PCR analysis and ELISA; whereas IFN-alpha and IFN-beta exerted virtually identical effects on transcriptome modulation, a differential gene regulation by type I and type II IFN emerged, especially as far as quantitative aspects were concerned. In vivo, IFN-alpha-producing tumors over-expressed murine CXCL10-11, GBP-1 and TRAIL, with evidence of CXCL11 production by tumor-associated EC. Overall, these findings improve our understanding of the anti-angiogenic effects of IFNs by showing that these cytokines trigger an anti-angiogenic transcriptional program in EC. Moreover, we suggest that quantitative differences in the magnitude of the transcriptional activation of IFNresponsive genes could form the basis for cell-specific transcriptional signatures.


description_brief: Genes up-regulated in endothelial cells: untreated versus exposed to E. burgdoferi.
systematic_name: M6707
exact_source: GSE6092_3465_200_UP
source_species_code: HS
GEO_id: GSE6092
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Borrelia burgdorferi, the agent of Lyme disease, promotes pro-inflammatory changes in endothelium that lead to the recruitment of leukocytes. The host immune response to infection results in increased levels of IFN-gamma in the serum and lesions of Lyme disease patients that correlate with greater severity of disease. Therefore, the effect of IFN-gamma on the gene expression profile of primary human endothelial cells exposed to B. burgdorferi was determined. B. burgdorferi and IFN-gamma synergistically augmented the expression of 34 genes, seven of which encode chemokines. Six of these (CCL7, CCL8, CX3CL1, CXCL9, CXCL10, and CXCL11) attract T lymphocytes, and one (CXCL2) is specific for neutrophils. Synergistic production of the attractants for T cells was confirmed at the protein level. IL-1beta, TNF-alpha, and LPS also cooperated with IFN-gamma to induce synergistic production of CXCL10 by endothelium, indicating that IFN-gamma potentiates inflammation in concert with a variety of mediators. An in vitro model of the blood vessel wall revealed that an increased number of human T lymphocytes traversed endothelium exposed to B. burgdorferi and IFN-gamma, as compared to unstimulated endothelial monolayers. In contrast, addition of IFN-gamma diminished the migration of neutrophils across B. burgdorferi-activated endothelium. IFN-gamma thus alters gene expression by endothelium exposed to B. burgdorferi in a manner that promotes recruitment of T cells and suppresses that of neutrophils. This modulation may facilitate the development of chronic inflammatory lesions in Lyme disease.


systematic_name: M6716
exact_source: GSE6092_3468_200_UP
source_species_code: HS
GEO_id: GSE6092
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in endothelial cells: B. burgdoferi versus IFNG [GeneID=3459] and B. burgdoferi .

description_full:
[cell repeats an earlier one in this file: 1603 characters]


systematic_name: M6717
exact_source: GSE6092_3468_200_DN
source_species_code: HS
GEO_id: GSE6092
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in endothelial cells: B. burgdoferi versus IFNG [GeneID=3459] and B. burgdoferi .

description_full:
[cell repeats an earlier one in this file: 1603 characters]


systematic_name: M6718
exact_source: GSE6092_3469_200_UP
source_species_code: HS
GEO_id: GSE6092
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in endothelial cells: IFNG [GeneID=3459] versus IFNG [GeneID=3459] and B. burgdoferi.

description_full:
[cell repeats an earlier one in this file: 1603 characters]


systematic_name: M6720
exact_source: GSE6092_3469_200_DN
source_species_code: HS
GEO_id: GSE6092
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in endothelial cells: IFNG [GeneID=3459] versus IFNG [GeneID=3459] and B. burgdoferi.

description_full:
[cell repeats an earlier one in this file: 1603 characters]


systematic_name: M6721
exact_source: GSE6259_2678_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in 33D1+ spleen dendritic cells: Flt3L Melanom injected mice versus healthy controls.

description_full:
  Dendritic cells (DCs) process and present self and foreign antigens to induce tolerance or immunity. In vitro models suggest that induction of immunity is controlled by regulating the presentation of antigen, but little is known about how DCs control antigen presentation in vivo. To examine antigen processing and presentation in vivo we specifically targeted antigens to the two major subsets of DCs using chimeric monoclonal antibodies. Unlike CD8+ DCs that express the cell surface protein CD205, CD8- DCs, which are positive for the 33D1 antigen, are specialized for presentation on MHC class II. This difference in antigen processing is intrinsic to the DC subsets and associated with increased expression of proteins associated with MHC processing.


systematic_name: M6722
exact_source: GSE6259_2678_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in 33D1+ spleen dendritic cells: Flt3L Melanom injected mice versus healthy controls.

description_full:
  Dendritic cells (DCs) process and present self and foreign antigens to induce tolerance or immunity. In vitro models suggest that induction of immunity is controlled by regulating the presentation of antigen, but little is known about how DCs control antigen presentation in vivo. To examine antigen processing and presentation in vivo we specifically targeted antigens to the two major subsets of DCs using chimeric monoclonal antibodies. Unlike CD8+ DCs that express the cell surface protein CD205, CD8- DCs, which are positive for the 33D1 antigen, are specialized for presentation on MHC class II. This difference in antigen processing is intrinsic to the DC subsets and associated with increased expression of proteins associated with MHC processing.


systematic_name: M6723
exact_source: GSE6259_2679_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleen dendritic cells from Flt3L Melanom injected mice: 33D1+ versus DEC205+ subpopulations.

description_full:
  Dendritic cells (DCs) process and present self and foreign antigens to induce tolerance or immunity. In vitro models suggest that induction of immunity is controlled by regulating the presentation of antigen, but little is known about how DCs control antigen presentation in vivo. To examine antigen processing and presentation in vivo we specifically targeted antigens to the two major subsets of DCs using chimeric monoclonal antibodies. Unlike CD8+ DCs that express the cell surface protein CD205, CD8- DCs, which are positive for the 33D1 antigen, are specialized for presentation on MHC class II. This difference in antigen processing is intrinsic to the DC subsets and associated with increased expression of proteins associated with MHC processing.


systematic_name: M6728
exact_source: GSE6259_2679_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen dendritic cells from Flt3L Melanom injected mice: 33D1+ versus DEC205+ subpopulations.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6730
exact_source: GSE6259_2680_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleen dendritic cells from healthy mice: 33D1+ versus DEC205+ subpopulations.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6731
exact_source: GSE6259_2680_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleen dendritic cells from healthy mice: 33D1+ versus DEC205+ subpopulations.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6746
exact_source: GSE6259_2685_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cells from Flt3L Melanom injected mice: 33D1+ versus CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6747
exact_source: GSE6259_2685_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cells from Flt3L Melanom injected mice: 33D1+ versus CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6760
exact_source: GSE6259_2690_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus B lymphocytes.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6762
exact_source: GSE6259_2690_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus B lymphocytes.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6763
exact_source: GSE6259_2691_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6764
exact_source: GSE6259_2691_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus CD4 [GeneID=920] T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6765
exact_source: GSE6259_2692_200_UP
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus CD8 T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


systematic_name: M6769
exact_source: GSE6259_2692_200_DN
source_species_code: MM
GEO_id: GSE6259
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in cells from Flt3L Melanom injected mice: splenic DEC205+ dendritic cells versus CD8 T cells.

description_full:
[cell repeats an earlier one in this file: 755 characters]


description_brief: Genes up-regulated in T reg: FOX3P [GeneID=50943] knockout versus wildtype.
systematic_name: M6777
exact_source: GSE6681_2641_200_UP
source_species_code: MM
GEO_id: GSE6681
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  Analysis of Foxp3 ablated peripheral regulatory T cells. Regulatory T cells require the expression of the transcription factor Foxp3 for thymic development. It is not known whether continuous expression of Foxp3 is required for the maintained function of mature regulatory T cells in the periphery. Results indicate changes to the regulatory T cell developmental program in the absence of Foxp3.


systematic_name: M6780
exact_source: GSE3203_2811_200_UP
source_species_code: MM
GEO_id: GSE3203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymph node B lymphocytes with influenza infection: wildtype versus IFNAR1 [GeneID=2454] knockout.

description_full:
  Influenza virus infection-induced gene expression changes of regional B cells are mediated at least in part through type I Interferon: Our objective is to determine whether the influenza virus-infection induced gene expression changes in regional lymph node B cells are facilitated at least in part through type I interferon. Our specific aim is to compare the gene expression profile of highly FACS-purified B cells in the regional lymph nodes of wildtype and IFNR-/- mice prior to and 48h following infection with influenza virus infection and to contrast this expression profile with that of FACS-purified wildtype B cells activated in vitro with IFN-beta +/- anti-CD86 for 12h.


systematic_name: M6781
exact_source: GSE3203_2810_200_DN
source_species_code: MM
GEO_id: GSE3203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymph node B lymphocytes: influenza infected versus interferon beta stimulation.

description_full:
  Influenza virus infection-induced gene expression changes of regional B cells are mediated at least in part through type I Interferon: Our objective is to determine whether the influenza virus-infection induced gene expression changes in regional lymph node B cells are facilitated at least in part through type I interferon. Our specific aim is to compare the gene expression profile of highly FACS-purified B cells in the regional lymph nodes of wildtype and IFNR-/- mice prior to and 48h following infection with influenza virus infection and to contrast this expression profile with that of FACS-purified wildtype B cells activated in vitro with IFN-beta +/- anti-CD86 for 12h.


systematic_name: M6790
exact_source: GSE3203_2810_200_UP
source_species_code: MM
GEO_id: GSE3203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in lymph node B lymphocytes: influenza infected versus interferon beta stimulation.

description_full:
[cell repeats an earlier one in this file: 681 characters]


systematic_name: M6798
exact_source: GSE3203_2811_200_DN
source_species_code: MM
GEO_id: GSE3203
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in lymph node B lymphocytes with influenza infection: wildtype versus IFNAR1 [GeneID=2454] knockout.

description_full:
[cell repeats an earlier one in this file: 681 characters]


description_brief: Genes up-regulated in T conv versus T reg.
systematic_name: M6799
exact_source: GSE6875_2937_200_UP
source_species_code: MM
GEO_id: GSE6875
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  To analyze gene expression in in regulatory T cell precursors that develop in the absence of a functional Foxp3 protein as compared to that of normal regulatory T cells


description_full: IgG cytoplasmic tail interferes with the induction of antigen-response genes
systematic_name: M6807
exact_source: GSE7218_3560_200_UP
source_species_code: MM
GEO_id: GSE7218
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes treated by anti-HEL and expressing BCR [GeneID=613] fusions with: IgM versus IgMG.


description_full: IgG cytoplasmic tail interferes with the induction of antigen-response genes
systematic_name: M6808
exact_source: GSE7218_3560_200_DN
source_species_code: MM
GEO_id: GSE7218
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes treated by anti-HEL and expressing BCR [GeneID=613] fusions with: IgM versus IgMG.


description_full: IgG cytoplasmic tail interferes with the induction of antigen-response genes
systematic_name: M6809
exact_source: GSE7218_3561_200_UP
source_species_code: MM
GEO_id: GSE7218
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in B lymphocytes: expressing IgM BCR [GeneID=613] fusion and untreated versus expressing IgMG BCR [GeneID=613] fusion and treated by anti-HEL.


description_full: IgG cytoplasmic tail interferes with the induction of antigen-response genes
systematic_name: M6810
exact_source: GSE7218_3561_200_DN
source_species_code: MM
GEO_id: GSE7218
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in B lymphocytes: expressing IgM BCR [GeneID=613] fusion and untreated versus expressing IgMG BCR [GeneID=613] fusion and treated by anti-HEL.


systematic_name: M6811
exact_source: GSE6090_2631_200_UP
source_species_code: HS
GEO_id: GSE6090
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in dendritic cells: control versus stimulated with anti-CD209 [GeneID=30835] antibody.

description_full:
  DC-SIGN is a C-type lectin expressed by dendritic cells (DCs) that binds HIV-1, sequestering it within multivesicular bodies to facilitate transmission to CD4+ T cells. Here we characterize the molecular basis of signalling through DC-SIGN by large-scale gene expression profiling and phosphoproteome analysis. Solitary DC-SIGN activation leads to a phenotypically disparate transcriptional program from Toll-like receptor (TLR) triggering with downregulation of MHC II, CD86, and interferon response genes and with induction of the TLR negative regulator ATF3. Phosphoproteome analysis reveals DC-SIGN signals through the leukemia-associated Rho guanine nucleotide exchange factor (LARG) to induce Rho activity. This LARG activation also occurs on DC HIV exposure and is required for effective HIV viral synapse formation. Taken together HIV mediated DC-SIGN signalling provides a mechanism by which HIV evades the immune response yet induces viral spread.


systematic_name: M6812
exact_source: GSE6090_2631_200_DN
source_species_code: HS
GEO_id: GSE6090
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in dendritic cells: control versus stimulated with anti-CD209 [GeneID=30835] antibody.

description_full:
  DC-SIGN is a C-type lectin expressed by dendritic cells (DCs) that binds HIV-1, sequestering it within multivesicular bodies to facilitate transmission to CD4+ T cells. Here we characterize the molecular basis of signalling through DC-SIGN by large-scale gene expression profiling and phosphoproteome analysis. Solitary DC-SIGN activation leads to a phenotypically disparate transcriptional program from Toll-like receptor (TLR) triggering with downregulation of MHC II, CD86, and interferon response genes and with induction of the TLR negative regulator ATF3. Phosphoproteome analysis reveals DC-SIGN signals through the leukemia-associated Rho guanine nucleotide exchange factor (LARG) to induce Rho activity. This LARG activation also occurs on DC HIV exposure and is required for effective HIV viral synapse formation. Taken together HIV mediated DC-SIGN signalling provides a mechanism by which HIV evades the immune response yet induces viral spread.


description_brief: Genes up-regulated in immature dendritic cells: untreated versus interferon alpha.
systematic_name: M6814
exact_source: GSE7509_3402_200_UP
source_species_code: HS
GEO_id: GSE7509
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The ability of dendritic cells (DCs) to activate immunity is linked to their maturation status. In prior studies we have shown that selective antibody-mediated blockade of inhibitory FcgRIIB receptor on human DCs in the presence of activating immunoglobulin (Ig) ligands leads to DC maturation and enhanced immunity to antibody-coated tumor cells. Here we show that Fcg receptor (FcgR) mediated activation of human monocytes and monocyte-derived DCs is associated with a distinct gene expression pattern, including several inflammation associated chemokines as well as type 1 interferon (IFN) response genes including the activation of signal transducer and activator of transcription 1 (STAT1).


description_full: Mice were immunized with PCC (pigeon cytochrome c).
systematic_name: M6836
exact_source: GSE7548_2702_200_UP
source_species_code: MM
GEO_id: GSE7548
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from lymph nodes: naïve versus day 7 after immunization.


description_full: Mice were immunized with PCC (pigeon cytochrome c).
systematic_name: M6837
exact_source: GSE7548_2702_200_DN
source_species_code: MM
GEO_id: GSE7548
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from lymph nodes: naïve versus day 7 after immunization.


description_full: Mice were immunized with PCC (pigeon cytochrome c).
systematic_name: M6839
exact_source: GSE7548_2703_200_UP
source_species_code: MM
GEO_id: GSE7548
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in CD4 [GeneID=920] T cells from lymph nodes: naïve versus day 28 after immunization.


description_full: Mice were immunized with PCC (pigeon cytochrome c).
systematic_name: M6841
exact_source: GSE7548_2703_200_DN
source_species_code: MM
GEO_id: GSE7548
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in CD4 [GeneID=920] T cells from lymph nodes: naïve versus day 28 after immunization.


description_brief: Genes up-regulated in macrophages: untreated versus LPS.
systematic_name: M6844
exact_source: GSE7348_3131_200_UP
source_species_code: MM
GEO_id: GSE7348
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_full:
  The inflammatory response initiated by microbial products signaling through Toll-like receptors (TLRs) of the innate immune system is essential for host defense against infection. Because inflammation can be harmful to host tissues, the innate response is highly regulated. Negative regulation of TLR4, the receptor for bacterial lipopolysaccharide (LPS), results in LPS tolerance, defined as hyporesponsiveness to repeated stimulation with LPS. LPS tolerance is thought to protect the host from excessive inflammation by turning off TLR4 signal, which then shuts down TLR-induced genes. However, TLR signaling induces hundreds of genes with very different functions. We reasoned that genes with different functions should have different requirements for regulation. Specifically, genes encoding proinflammatory mediators should be transiently inactivated to limit tissue damage, while genes encoding antimicrobial effectors, which directly target pathogens, should remain inducible in tolerant cells to protect the host from infection. Using an in vitro system of LPS tolerance in macrophages, here we show that TLR-induced genes may indeed be divided into two distinct categories based on their functions and regulatory requirements. Further, we show these distinct groups are regulated by gene-specific, and not signal-specific mechanisms.


systematic_name: M6851
exact_source: GSE7768_2696_200_UP
source_species_code: MM
GEO_id: GSE7768
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleens from mice immunized with ova peptides alone versus those immunized with LPS as adjuvant.

description_full:
  An unresolved issue in immunology is the extent to which inflammatory effects are needed for robust T cell responses. In this study, mice were immunized by iv injection using either high toxicity lipopolysaccharide (LPS) or low toxicity monophosphoryl lipid A (MPL) as adjuvant. Six hours after iv immunization, whole spleens were harvested and gene expression was measured in unfractionated splenic populations of cells. The analysis indicated that the low toxicity adjuvanticity of MPL was associated with TLR4-mediated signaling that was biased to the TRIF branch of TLR4, while LPS generated balanced MyD88 and TRIF-associated outcomes.


systematic_name: M6852
exact_source: GSE7768_2696_200_DN
source_species_code: MM
GEO_id: GSE7768
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleens from mice immunized with ova peptides alone versus those immunized with LPS as adjuvant.

description_full:
  An unresolved issue in immunology is the extent to which inflammatory effects are needed for robust T cell responses. In this study, mice were immunized by iv injection using either high toxicity lipopolysaccharide (LPS) or low toxicity monophosphoryl lipid A (MPL) as adjuvant. Six hours after iv immunization, whole spleens were harvested and gene expression was measured in unfractionated splenic populations of cells. The analysis indicated that the low toxicity adjuvanticity of MPL was associated with TLR4-mediated signaling that was biased to the TRIF branch of TLR4, while LPS generated balanced MyD88 and TRIF-associated outcomes.


systematic_name: M6857
exact_source: GSE7768_2698_200_UP
source_species_code: MM
GEO_id: GSE7768
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes up-regulated in spleens from mice immunized with ova peptides alone versus those immunized with monophosphoryl lipid A as adjuvant.

description_full:
[cell repeats an earlier one in this file: 640 characters]


systematic_name: M6859
exact_source: GSE7768_2698_200_DN
source_species_code: MM
GEO_id: GSE7768
contributor: Jernej Godec
contrib_organization: Dana-Farber Cancer Institute
description_brief:
  Genes down-regulated in spleens from mice immunized with ova peptides alone versus those immunized with monophosphoryl lipid A as adjuvant.

description_full:
[cell repeats an earlier one in this file: 640 characters]


description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6867
exact_source: GSE4590_3551_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: pre-B I versus VPREB1+ [GeneID=7441] large pre-B II.


description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6871
exact_source: GSE4590_3551_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: pre-B I versus VPREB1+ [GeneID=7441] large pre-B II.


description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6874
exact_source: GSE4590_3553_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: small pre-B II versus VPREB1+ [GeneID=7441] large pre-B II.


description_full: Cells from four develppmental stages were purified by FACS from human bone marrow samples
systematic_name: M6876
exact_source: GSE4590_3553_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: small pre-B II versus VPREB1+ [GeneID=7441] large pre-B II.


