Supplemental Table. Unabridged List of Genes Differentially Expressed Between AD and AI Prostate Cancer (Best, C.J.M., et al.) Gene Symbol Probe Set Fold Change Parametric Description Map GenBank UniGene AI/AD p-value Accession Cluster AP2A2 215764_x_at 0.60 0.0001 adaptor-related protein complex 2, alpha 2 subunit 11p15.5 AA877641 Hs.19121 ADORA2A 205013_s_at 0.69 0.0030 adenosine A2a receptor 22q11.23 NM_000675.2 Hs.197029 ADPRTL2 215773_x_at 1.41 0.0039 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2 14q11.2-q12 AJ236912.1 Hs.409412 AKR7A2 202139_at 0.62 0.0006 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde 1p35.1-p36.23 NM_003689.1 Hs.6980 reductase) STAT5B 212550_at 0.71 0.0001 signal transducer and activator of transcription 5B 17q11.2 AL080218.1 Hs.434992 ST3GALVI 213355_at 3.44 0.0045 alpha2,3-sialyltransferase 3q12.2 AK001922.1 Hs.440913 A2M 217757_at 2.07 0.0030 alpha-2-macroglobulin 12p13.3-p12.3 NM_000014.3 Hs.74561 ALS2CR3 202125_s_at 1.72 0.0006 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, 2q33 NM_015049.1 Hs.154248 candidate 3 ASPN 219087_at 2.87 0.0017 asporin (LRR class 1) 9q22 NM_017680.1 Hs.435655 ATP5L 208746_x_at 0.68 0.0030 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g 11q23 AF070655.1 Hs.107476 ATP6V0B 200078_s_at 0.60 0.0018 ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c'' 1p32.3 BC005876.1 Hs.7476 ABCG2 209735_at 1.87 0.0014 ATP-binding cassette, sub-family G (WHITE), member 2 4q22 AF098951.2 Hs.194720 BAIAP2 209502_s_at 0.40 0.0012 BAI1-associated protein 2 17q25 BC002495.1 Hs.188332 BLZF1 32088_at 2.67 0.0025 basic leucine zipper nuclear factor 1 (JEM-1) 1q24 U79751 Hs.444697 BCKDK 202030_at 0.57 0.0004 branched chain alpha-ketoacid dehydrogenase kinase 16p11.2 NM_005881.1 Hs.20644 BIN3 222199_s_at 0.62 0.0027 bridging integrator 3 8p21.2 AK001289.1 Hs.68090 BTG2 201236_s_at 0.50 0.0021 BTG family, member 2 1q32 NM_006763.1 Hs.75462 BPAG1 212254_s_at 2.78 0.0001 bullous pemphigoid antigen 1, 230/240kDa 6p12-p11 BG253119 Hs.443518 BPAG1 215016_x_at 2.54 0.0002 bullous pemphigoid antigen 1, 230/240kDa 6p12-p11 BC004912.1 Hs.443518 SHAPY 46323_at 0.57 0.0046 Ca2+-dependent endoplasmic reticulum nucleoside diphosphatase 17q25.3 AL120741 Hs.8859 CDH11 207173_x_at 3.10 0.0004 cadherin 11, type 2, OB-cadherin (osteoblast) 16q22.1 D21254.1 Hs.443435 CPT2 204264_at 0.60 0.0026 carnitine palmitoyltransferase II 1p32 NM_000098.1 Hs.274336 CD84 211189_x_at 0.58 0.0032 CD84 antigen (leukocyte antigen) 1q24 AF054816.1 Hs.398093 GRIM19 220864_s_at 0.21 0.0020 cell death-regulatory protein GRIM19 19p13.2 NM_015965.1 Hs.279574 CGI-12 219363_s_at 2.54 0.0030 CGI-12 protein 8q22.1 NM_015942.1 Hs.46680 CGI-130 203259_s_at 1.61 0.0038 CGI-130 protein 6q13-q24.3 BC001671.1 Hs.32826 PNAS-4 212371_at 1.92 0.0003 CGI-146 protein 1q44 AL049397.1 Hs.211473 CCR9 207445_s_at 0.65 0.0031 chemokine (C-C motif) receptor 9 3p21.3 AF145439.1 Hs.225946 CXCR6 206974_at 0.67 0.0039 chemokine (C-X-C motif) receptor 6 3p21 NM_006564.1 Hs.34526 CSPG2 204619_s_at 3.10 0.0010 chondroitin sulfate proteoglycan 2 (versican) 5q14.3 BF590263 Hs.434488 C11orf10 218213_s_at 0.46 0.0023 chromosome 11 open reading frame 10 11q12-q13.1 NM_014206.1 Hs.437779 C11orf2 217969_at 0.63 0.0018 chromosome 11 open reading frame2 11q13 NM_013265.2 Hs.277517 C14orf2 210532_s_at 0.68 0.0033 chromosome 14 open reading frame 2 14q32.33 AF116639.1 Hs.109052 C14orf58 219316_s_at 0.67 0.0032 chromosome 14 open reading frame 58 14q24.3 NM_017791.1 Hs.267566 C2orf3 216305_s_at 1.72 0.0021 chromosome 2 open reading frame 3 2p11.2-p11.1 AC005034 Hs.158969 C21orf97 218018_at 0.58 0.0048 chromosome 21 open reading frame 97 21q22.3 NM_021941.1 Hs.458335 C22orf4 33778_at 0.67 0.0008 chromosome 22 open reading frame 4 22q13.3 AL096779 Hs.20017 C5orf6 218023_s_at 0.62 0.0008 chromosome 5 open reading frame 6 5q31 NM_016605.1 Hs.54056 LUC7A 220044_x_at 2.75 0.0007 cisplatin resistance-associated overexpressed protein 17q21 NM_016424.1 Hs.130293 COL5A2 221729_at 2.30 0.0043 collagen, type V, alpha 2 2q14-q32 NM_000393.1 Hs.283393 COL15A1 203477_at 2.67 0.0006 collagen, type XV, alpha 1 9q21-q22 NM_001855.1 Hs.409034 COPS6 213504_at 0.72 0.0032 COP9 subunit 6 (MOV34 homolog, 34 kD) 7q22.1 W63732 Hs.15591 CXADR 203917_at 0.57 0.0048 coxsackie virus and adenovirus receptor 21q21.1 NM_001338.1 Hs.79187 DMTF1 203301_s_at 1.90 0.0012 cyclin D binding myb-like transcription factor 1 7q21 NM_021145.1 Hs.129506 COX7C 217491_x_at 0.51 0.0041 cytochrome c oxidase subunit VIIc 5q14 AF042165 Hs.430075 COX8 201119_s_at 0.57 0.0024 cytochrome c oxidase subunit VIII 11q12-q13 NM_004074.1 Hs.433901 DBP 209783_at 0.63 0.0003 D site of albumin promoter (albumin D-box) binding protein 19q13.3 D28468.1 Hs.414480 DC13 218447_at 0.52 0.0035 DC13 protein 16q23.2 NM_020188.1 Hs.6879 DSS1 202276_at 0.63 0.0040 Deleted in split-hand/split-foot 1 region 7q21.3-q22.1 NM_006304.1 Hs.333495 DBI 209389_x_at 0.58 0.0001 diazepam binding inhibitor (GABA receptor modulator, acyl- 2q12-q21 M15887.1 Hs.78888 Coenzyme A binding protein) DKFZp547P234 221865_at 0.64 0.0040 DKFZp547P234 protein 9q33.1 BF969986 Hs.170226 DKFZP564O0823 204687_at 0.58 0.0008 DKFZP564O0823 protein 4q13.3-q21.3 NM_015393.1 Hs.105460 DKFZP566H073 212047_s_at 0.72 0.0049 DKFZP566H073 protein 17p13.3 AK025329.1 Hs.7158 EDG4 206723_s_at 0.57 0.0043 endothelial differentiation, lysophosphatidic acid G-protein-coupled 19p12 AF011466.1 Hs.122575 receptor, 4 EIF3S9 203462_x_at 0.65 0.0001 eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa 7p22.3 NM_003751.1 Hs.371001 EIF4EL3 213571_s_at 0.73 0.0027 eukaryotic translation initiation factor 4E-like 3 2q37.1 BF516289 Hs.211823 XPO1 208775_at 1.62 0.0046 exportin 1 (CRM1 homolog, yeast) 2p16 D89729.1 Hs.157367 ECM2 206101_at 2.25 0.0040 extracellular matrix protein 2, female organ and adipocyte specific 9q22.3 NM_001393.1 Hs.117060 FBXO11 203255_at 1.95 0.0009 F-box only protein 11 2p21 NM_018693.1 Hs.284289 FBXO3 218432_at 2.10 0.0049 F-box only protein 3 11p13 NM_012175.1 Hs.406787 FN1 212464_s_at 2.53 0.0005 fibronectin 1 2q34 X02761.1 Hs.418138 FN1 211719_x_at 2.72 0.0007 fibronectin 1 2q34 BC005858.1 Hs.418138 FN1 210495_x_at 1.86 0.0013 fibronectin 1 2q34 AF130095.1 Hs.418138 FRAT2 209864_at 0.65 0.0017 frequently rearranged in advanced T-cell lymphomas 2 10q24.1 AB045118.1 Hs.140720 X123 213900_at 0.34 0.0011 Friedreich ataxia region gene X123 9q13-q21 AA524029 Hs.77889 GPR116 212950_at 2.40 0.0044 G protein-coupled receptor 116 6p21.1 AB018301.1 Hs.362806 GABARAPL3 211458_s_at 0.52 0.0014 GABA(A) receptors associated protein like 3 15q26.1 AF180519.1 Hs.334497 GMPPB 219920_s_at 0.63 0.0019 GDP-mannose pyrophosphorylase B 3p21.31 NM_021971.1 Hs.438691 GTF3C3 218343_s_at 1.60 0.0033 general transcription factor IIIC, polypeptide 3, 102kDa 2q33.1 NM_012086.1 Hs.253724 GL004 219137_s_at 1.69 0.0015 GL004 protein 2q36.3 NM_020194.1 Hs.105166 G6PT1 202830_s_at 0.58 0.0024 glucose-6-phosphatase, transport (glucose-6-phosphate) protein 1 11q23.3 NM_001467.1 Hs.132760 GFPT1 202721_s_at 0.60 0.0006 glutamine-fructose-6-phosphate transaminase 1 2p13 BE645771 Hs.1674 GREB1 205862_at 0.18 0.0019 GREB1 protein 2p25.1 NM_014668.1 Hs.438037 GADD45B 209304_x_at 0.26 0.0030 growth arrest and DNA-damage-inducible, beta 19p13.3 AF087853.1 Hs.110571 GADD45B 207574_s_at 0.28 0.0031 growth arrest and DNA-damage-inducible, beta 19p13.3 NM_015675.1 Hs.110571 GADD45G 204121_at 0.23 0.0001 growth arrest and DNA-damage-inducible, gamma 9q22.1-q22.2 NM_006705.2 Hs.9701 GMPR 204187_at 0.57 0.0036 guanosine monophosphate reductase 6p23 NM_006877.1 Hs.1435 HNRPA0 201055_s_at 0.65 0.0007 heterogeneous nuclear ribonucleoprotein A0 5q31 NM_006805.1 Hs.96996 HNRPH3 208990_s_at 1.73 0.0011 heterogeneous nuclear ribonucleoprotein H3 (2H9) 10q22 AF132362.1 Hs.156481 D13S106E 204190_at 1.80 0.0002 highly charged protein 13q12-q14 NM_005800.1 Hs.291431 HINT1 208826_x_at 0.66 0.0007 histidine triad nucleotide binding protein 1 5q31.2 U27143.1 Hs.256697 HOP 211597_s_at 1.89 0.0028 homeodomain-only protein 4q11-q12 AB059408.1 Hs.13775 222148_s_at 1.27 0.0015 Homo sapiens mRNA; cDNA DKFZp434I212 (from clone 17 BF688108 Hs.436453 DKFZp434I212) 221844_x_at 0.50 0.0000 Homo sapiens transcribed sequence with moderate similarity to 4 AV756161 Hs.508129 protein ref:NP_060312.1 (H.sapiens) hypothetical protein FLJ20489 [Homo sapiens] 213931_at 0.29 0.0017 Homo sapiens transcribed sequence with strong similarity to protein AI819238 Hs.502810 pir:A40227 (H.sapiens) A40227 transcription repressor Id-2 - human 215088_s_at 0.78 0.0034 Homo sapiens transcribed sequence with strong similarity to protein BG110532 Hs.355964 ref:NP_002992.1 (H.sapiens) succinate dehydrogenase complex, subunit C precursor; Succinate dehydrogenase complex, subunit C, integral membrane protein,; succinate-ubiquinone oxidoreduca 214351_x_at 0.45 0.0020 Homo sapiens transcribed sequence with strong similarity to protein 16 AA789278 Hs.410817 ref:NP_150254.1 (H.sapiens) ribosomal protein L13; 60S ribosomal protein L13; breast basic conserved protein 1 [Homo sapiens] 55705_at 0.70 0.0048 Homo sapiens transcribed sequences W07773 Hs.498224 221803_s_at 2.44 0.0023 Homo sapiens, nuclear receptor binding factor-2, clone 10 AA883074 Hs.27181 IMAGE:3463191, mRNA HERPUD1 217168_s_at 0.72 0.0012 homocysteine-inducible, endoplasmic reticulum stress-inducible, 16q12.2-q13 AF217990.1 Hs.146393 ubiquitin-like domain member 1 HGD 214307_at 0.33 0.0001 homogentisate 1,2-dioxygenase (homogentisate