Affymetrix These are the files where locus mappings are taken from at http://www.affymetrix.com/analysis/downloads/expression_array_bed_files: HC-G110.bed.gz HG-Focus.bed.gz HG-U133_PLUS_2.bed.gz HG-U133A.bed.gz HG-U133B.bed.gz HG-U95A.bed.gz HG-U95Av2.bed.gz HG-U95B.bed.gz HG-U95C.bed.gz HG-U95D.bed.gz HG-U95E.bed.gz Hu35KsubA.bed.gz Hu35KsubB.bed.gz Hu35KsubC.bed.gz Hu35KsubD.bed.gz HuGeneFL.bed.gz MG_U74A.bed.gz MG_U74Av2.bed.gz MG_U74B.bed.gz MG_U74Bv2.bed.gz MG_U74C.bed.gz MG_U74Cv2.bed.gz MG-U74A.bed.gz MG-U74Av2.bed.gz MG-U74B.bed.gz MG-U74Bv2.bed.gz MG-U74C.bed.gz MG-U74Cv2.bed.gz MOE430A.bed.gz MOE430B.bed.gz Mouse430_2.bed.gz Mouse430A_2.bed.gz Mu11KsubA.bed.gz Mu11KsubB.bed.gz RAE230A.bed.gz RAE230B.bed.gz Rat230_2.bed.gz RG-U34A.bed.gz RG-U34B.bed.gz RG-U34C.bed.gz RN-U34.bed.gz RT-U34.bed.gz U133_X3P.bed.gz The gene mappings are taken from the annotations provided on the Affymetrix website at: http://www.affymetrix.com/support/technical/annotationfilesmain.affx ATH1-121501.na28.annot.csv Barley1.na28.annot.csv Bovine.na28.annot.csv Canine.na28.annot.csv Canine_2.na28.annot.csv Celegans.na28.annot.csv Chicken.na28.annot.csv Citrus.na28.annot.csv Cotton.na28.annot.csv DrosGenome1.na28.annot.csv Drosophila_2.na28.annot.csv E_coli_2.na28.annot.csv Ecoli_ASv2.na28.annot.csv HG_U95A.na28.annot.csv HG_U95Av2.na28.annot.csv HG_U95B.na28.annot.csv HG_U95C.na28.annot.csv HG_U95D.na28.annot.csv HG_U95E.na28.annot.csv HG-Focus.na28.annot.csv HG-U133_Plus_2.na28.annot.csv HG-U133A.na28.annot.csv HG-U133A_2.na28.annot.csv HG-U133B.na28.annot.csv HT_HG-U133_Plus_PM.na28.annot.csv HT_HG-U133A.na28.annot.csv HT_HG-U133B.na28.annot.csv HT_Rat230_PM.na28.annot.csv HT_Rat-Focus.na28.annot.csv Maize.na28.annot.csv Medicago.na28.annot.csv MOE430A.na28.annot.csv MOE430B.na28.annot.csv Mouse430_2.na28.annot.csv Mouse430A_2.na28.annot.csv Pae_G1a.na28.annot.csv Plasmodium_Anopheles.na28.annot.csv Poplar.na28.annot.csv Porcine.na28.annot.csv RAE230A.na28.annot.csv RAE230B.na28.annot.csv Rat230_2.na28.annot.csv RatToxFX.na28.annot.csv RG_U34A.na28.annot.csv RG_U34B.na28.annot.csv RG_U34C.na28.annot.csv Rice.na28.annot.csv RT_U34.na28.annot.csv S_aureus.na28.annot.csv Soybean.na28.annot.csv Sugar_Cane.na28.annot.csv Test3.na28.annot.csv Tomato.na28.annot.csv U133_X3P.na28.annot.csv Vitis_Vinifera.na28.annot.csv wheat.na28.annot.csv X_laevis_2.na28.annot.csv X_tropicalis.na28.annot.csv Xenopus_laevis.na28.annot.csv Yeast_2.na28.annot.csv YG_S98.na28.annot.csv Zebrafish.na28.annot.csv Agilent: Below are the files used for Agilent mappings taken from http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp58802.aspx The columns used were ProbeID and either GenomicCoordinates if available or GeneSymbol: Arabidopsis, 021169_D_AA_20080807.txt Barley, 021623_D_AA_20081002.txt Bovine, 015354_D_GeneList_20061130.txt C.elegans_V2, 020186_D_AA_20080509.txt Chicken, 015068_D_AA_20060913.txt Dog_V2, 015067_D_AA_20060913.txt Drosophilia, 018972_D_AA_20080117.txt E.coli, 020097_D_AA_20080430.txt Frog, 015066_D_AA_20060913.txt Horse, 021322_D_AA_20080827.txt Human_Genome, 014850_D_AA_20070820.txt M.grisea, 015060_D_AA_20060913.txt Maize, 016047_D_GeneList_20070512.txt Mosquito, 020449_D_AA_20080612.txt Mouse_Development, 015062_D_AA_20060913.txt Mouse_Genome, 014868_D_GeneList_20070820.txt Porcine, 020109_D_AA_20080430.txt Rabbit, 020908_D_AA_20080722.txt Rat_Genome, 014879_D_AA_20070820.txt Rhesus_Monkey, 015421_D_GeneList_20061115.txt Salmon, 020938_D_AA_20080722.txt Sheep, 019921_D_AA_20080430.txt Tobacco, 021113_D_AA_20080801.txt Tomato, 022270_D_AA_20081211.txt Wheat, 022297_D_AA_20090105.txt Yeast_V2, 015072_D_AA_20060913.txt Zebrafish, 019161_D_AA_20080131.txt Illumina: Below are the files used for the Illumina probe mappings from http://www.switchtoi.com/annotationfiles.ilmn. The columns used were Probe_Id and either Probe_Coordinates if available or Symbol: HumanHT-12_V3_0_R2_11283641_A.txt HumanRef-8_V3_0_R2_11282963_A.txt HumanWG-6_V3_0_R2_11282955_A.txt MouseRef-8_V2_0_R2_11278551_A.txt MouseWG-6_V2_0_R2_11278593_A.txt RatRef-12_V1_0_R4_11222119_A.txt