Huang et al 2007

Supplementary Table S1. Clinical characteristics

Biopsy Surgery Patient Clinical PSA pre- che- PSA post- che- % PSA Age Gleason Gleason ID stage motherapy motherapy Change score score 6082-02 67 8 9 T3b 10.5 5.8 -44.8 6082-03 71 7 7 T3b 9.9 4.6 -53.5 6082-04 75 6 7 T2c 10.1 4.1 -59.4 6082-07 74 7 7 T3c 7.2 3.9 -45.8 6082-08 64 7 6 T3c 46.3 20.9 -54.9 6082-10 71 8 6 T2c 28.6 15.0 -47.6 6082-13 78 8 8 T3a 33.3 17.8 -46.5 6082-14 77 9 8 T3c 4.2 1.6 -61.9 6082-15 57 6 7 T3a 34.4 19.9 -42.2 6082-16 69 8 7 T2c 7.8 5.3 -32.1 6082-19 56 6 7 T2c 6.8 6.0 -11.8 6082-22 63 7 7 T2b 15.3 8.2 -46.4 6082-23 60 7 8 T2b 5.9 3.3 -44.1 6082-24 72 8 8 T3a 9.3 10.3 10.8 6082-25 67 9 7 T2c 6.5 9.8 50.8 6082-28 67 9 7 T3c 34.1 25.4 -25.5 6082-31 60 7 7 T3a 11.7 7.4 -36.8 6082-32 68 8 6 T2c 4.0 4.6 15.0 6082-34 68 9 9 T3b 35.3 19.3 -45.3 6082-36 66 8 9 T3b 5.0 3.7 -26.0 KP-01 59 7 6 T2a 12.2 9.8 -19.7 KP-02 65 7 7 T3b 13.2 10.7 -18.9 KP-03 59 7 7 T2a 1.4 0.8 -42.9 KP-04 73 7 7 T2c 3.1 4.0 29.0 KP-05 71 10 10 T3b 3.1 3.4 9.7 UW-01 65 7 7 T2c 37.3 38.7 3.8 UW-03 59 9 9 T4a 18.6 8.4 -54.8 UW-05 67 8 7 T2c 5.9 4.0 -32.2 UW-09 63 7 9 T3b 1.7 0.5 -70.6 UW-10 61 7 8 T2c 7.8 2.4 -69.2 UW-11 66 7 8 T2c 8.0 5.2 -35.0

Huang et al 2007

Supplementary Table S2. Chemotherapy-associated expression changes (p<0.01). Unigene HUGO Description Ratio* Hs.624 IL8 Interleukin 8 3.27 Hs.144513 TMEFF2 TM w/EGF-like, follistatin-like domains 2 2.39 Hs.303649 CCL2 Chemokine (C-C motif) ligand 2 2.18 Hs.466871 PLAUR Plasminogen activator urokinase receptor 2.05 Hs.413924 CXCL10 Chemokine (C-X-C motif) ligand 10 1.81 Hs.504609 ID1 Inhibitor of DNA binding 1 1.80 Hs.293736 ADNP Activity-dependent neuroprotector 1.74 Hs.515258 GDF15 Growth differentiation factor 15 1.71 Hs.502829 SF1 Splicing factor 1 1.61 Hs.76884 ID3 Inhibitor of DNA binding 3 1.56 Hs.76753 ENG Endoglin (Osler-Rendu-Weber syndrome 1) 1.50 Hs.472651 BLCAP Bladder cancer associated protein 1.49 Hs.2178 HIST2H2BE Histone 2 H2be 1.47 Hs.244139 TNFRSF6 TNF receptor superfamily member 6 1.46 Hs.2030 THBD Thrombomodulin 1.45 Hs.270055 SH3GL3 SH3-domain GRB2-like 3 1.44 Hs.126256 IL1B Interleukin 1 beta 1.43 Hs.549393 FOSL2 FOS-like antigen 2 1.41 Hs.520140 SRF Serum response factor 1.38 Hs.470943 STAT1 Signal transducer and activator of transcription 1 1.37 Hs.159161 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha 1.35 Hs.435490 TMPRSS7 Transmembrane protease, serine 7 1.34 Hs.59332 SPRED2 Sprouty-related EVH1 domain containing 2 1.34 Hs.405662 CRABP2 Cellular retinoic acid binding protein 2 1.33 Hs.516490 TANK TRAF family member-associated NFKB activator 1.33 Hs.429581 RTN4 Reticulon 4 1.32 Hs.380906 MYADM Myeloid-associated differentiation marker 1.30 Hs.501309 CIRBP Cold inducible RNA binding protein 1.29 Hs.512908 ARPP-19 Cyclic AMP phosphoprotein 19 kD 1.27 Hs.495960 ATP6AP2 ATPase H+ transporting lysosomal AP 2 1.26 Hs.487325 PRKACB Protein kinase cAMP-dependent catalytic beta 1.26 Hs.493096 PBX1 Pre-B-cell leukemia transcription factor 1 1.26 Hs.370725 OSBPL1A Oxysterol binding protein-like 1A 1.23 Hs.73799 GNAI3 Guanine nucleotide BP alpha inhibiting activity 3 1.22 Hs.534312 TOR1A Torsin family 1 member A (torsin A) 1.19 Hs.444600 LAT1-3TM LAT1-3TM protein 1.18 Hs.517948 DHX30 DEAH (Asp-Glu-Ala-His) box polypeptide 30 1.18 Hs.480073 HNRPD Heterogeneous nuclear ribonucleoprotein D 1.16 Hs.459779 DNAJA3 DnaJ (Hsp40) homolog subfamily A member 3 0.86 Hs.248785 AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 0.84 Hs.272062 PTPRF Protein tyrosine phosphatase receptor type F 0.84 Hs.433702 EIF5 Eukaryotic translation initiation factor 5 0.83 Hs.302977 C12orf4 12 open reading frame 4 0.82 Hs.25669 NCOA5 Nuclear receptor coactivator 5 0.79 Hs.356247 ACY1L2 Aminoacylase 1-like 2 0.79 Hs.301277 KIAA0543 KIAA0543 protein 0.79 Hs.524183 FKBP4 FK506 binding protein 4 59kDa 0.76 Hs.32417 SARG Specifically androgen-regulated protein 0.75 Hs.438545 SLC2A9 Solute carrier family 2, member 9 0.73 Hs.411490 FAM36A Family with sequence similarity 36 member A 0.72 Hs.284491 PDXK Pyridoxal (pyridoxine vitamin B6) kinase 0.68 Hs.302738 SLC26A2 Solute carrier family 26 member 2 0.63 Hs.533977 TXNIP Thioredoxin interacting protein 0.57 * Ratio = geometric means of fold difference between Post-treated and Pre-treated samples.

Huang et al 2007

Supplementary Table S3. with significantly altered expression including ischemia- related genes ordered by ratio in post-treated surgical prostatectomy specimens compared with pre-treated needle biopsy specimens. All p-values were less than 0.001 by random variance t- statistics by BRB 3.4 software.

Gene sym- Ischemia UG cluster Description Ratio* bol related Hs.171695 DUSP1 Dual specificity phosphatase 1 5.46 Yes Hs.527973 SOCS3 Suppressor of cytokine signaling 3 4.80 Yes Hs.444569 VMP1 ortholog of rat vacuole membrane protein 1 4.75 Yes Hs.25292 JUNB Jun B proto-oncogene 3.99 Yes Hs.525704 JUN V-jun sarcoma virus 17 oncogene homolog 3.88 Yes Hs.624 IL8 Interleukin 8 3.27 Hs.501629 IER2 Immediate early response 2 3.06 Yes Hs.410037 CTGF Connective tissue growth factor 2.98 Yes Hs.285313 KLF6 Kruppel-like factor 6 2.79 Yes Hs.512306 CCL4L1 Chemokine (C-C motif) ligand 4-like 1 2.66 Yes Hs.76095 IER3 Immediate early response 3 2.50 Hs.144513 TMEFF2 TM protein EGF-like, 2 follistatin-like domains 2.39 Hs.370771 CDKN1A Cyclin-dependent kinase inhibitor 1A (p21) 2.34 Yes Hs.303649 CCL2 Chemokine (C-C motif) ligand 2 2.33 Hs.421986 CXCR4 Chemokine (C-X-C motif) receptor 4 2.32 Yes Hs.519162 BTG2 BTG family member 2 2.29 Yes Hs.2780 JUND Jun D proto-oncogene 2.18 Yes Hs.534115 ADAMTS1 A disintegrin-like, MMP with thrombospondin 2.05 Hs.799 DTR Diphtheria toxin receptor 2.05 Yes Hs.466871 PLAUR Plasminogen activator urokinase receptor 2.05 Hs.502876 RHOB Ras homolog gene family member B 2.01 Yes Hs.504035 IL10RA Interleukin 10 receptor alpha 1.82 Hs.413924 CXCL10 Chemokine (C-X-C motif) ligand 10 1.81 Hs.504609 ID1 Inhibitor of DNA binding 1 1.80 Hs.532826 MCL1 Myeloid cell leukemia sequence 1 1.77 Yes Hs.376206 KLF4 Kruppel-like factor 4 (gut) 1.77 Yes Hs.419240 SLC2A3 Solute carrier family 2 member 3 1.76 Hs.293736 ADNP Activity-dependent neuroprotector 1.74 Hs.512683 CCL3L1 Chemokine (C-C motif) ligand 3-like 1 1.74 Hs.515258 GDF15 Growth differentiation factor 15 1.71 Hs.296169 RAB4A RAB4A member RAS oncogene family 1.71 Yes Hs.507916 TGFB1I4 TGFb induced transcript 4 1.68 Yes Hs.502829 SF1 Splicing factor 1 1.61 Hs.436061 IRF1 Interferon regulatory factor 1 1.60 Yes Hs.549488 LMO7 LIM domain 7 1.58 Hs.67928 ELF3 E74-like factor 3 1.57 Hs.76884 ID3 Inhibitor of DNA binding 3 1.56 Hs.5476 SLC25A25 Solute carrier family 25 member 25 1.52 Yes Hs.76753 ENG Endoglin (Osler-Rendu-Weber syndrome 1) 1.50 Hs.472651 BLCAP Bladder cancer ass. protein 1.49 Hs.2178 HIST2H2BE Histone 2 H2be 1.47 Hs.244139 TNFRSF6 Tumor necrosis factor receptor member 6 1.46 Hs.516664 EFNA1 Ephrin-A1 1.45 Yes Hs.2030 THBD Thrombomodulin 1.45 Hs.270055 SH3GL3 SH3-domain GRB2-like 3 1.44 Hs.520942 CLDN4 Claudin 4 1.43 Yes Hs.126256 IL1B Interleukin 1 beta 1.43 Hs.549393 FOSL2 FOS-like antigen 2 1.41 Hs.266826 ARMC8 Armadillo repeat containing 8 1.40 Hs.470887 GULP1 GULP engulfment adaptor PTB domain c 1 1.40 Hs.520140 SRF Serum response factor 1.38 Huang et al 2007

Hs.523968 TP53BP2 Tumor protein p53 binding protein 2 1.38 Hs.470943 STAT1 Signal transducer, activator of transcr 1 1.37 Hs.159161 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha 1.35 Hs.527412 ASAH1 N-acylsphingosine amidohydrolase 1.35 - - Homo sapiens 3 BAC RP11-307B9 1.34 Hs.59332 SPRED2 Sprouty-related EVH1 domain containing 2 1.34 Hs.520640 ACTB Actin beta 1.34 Yes Hs.369920 RAP1B RAP1B member of RAS oncogene family 1.34 Hs.405662 CRABP2 Cellular retinoic acid binding protein 2 1.33 Hs.516490 TANK TRAF family member-associated NFKB act 1.33 Hs.429581 RTN4 Reticulon 4 1.32 Hs.536535 DUSP16 Dual specificity phosphatase 16 1.30 Yes Hs.380906 MYADM Myeloid-associated differentiation marker 1.30 Hs.236828 WRNIP1 Werner interacting protein 1 1.29 Hs.501309 CIRBP Cold inducible RNA binding protein 1.29 Hs.512908 ARPP-19 Cyclic AMP phosphoprotein 19 kD 1.27 Hs.495960 ATP6AP2 ATPase H+ transporting lysosomal acc prot 2 1.26 Hs.487325 PRKACB Protein kinase cAMP-dependent catalytic beta 1.26 Hs.493096 PBX1 Pre-B-cell leukemia transcription factor 1 1.26 Hs.370725 OSBPL1A Oxysterol binding protein-like 1A 1.23 Hs.73799 GNAI3 GNBP alpha inhibiting activity polypeptide 3 1.22 Hs.534312 TOR1A Torsin family 1 member A (torsin A) 1.19 Hs.444600 LAT1-3TM LAT1-3TM protein 1.18 Hs.517948 DHX30 DEAH (Asp-Glu-Ala-His) box polypeptide 30 1.18 Hs.480073 HNRPD Heterogeneous nuclear ribonucleoprotein D 1.16 Hs.459779 DNAJA3 DnaJ (Hsp40) homolog subfamily A member 3 0.86 Hs.248785 AGPAT3 1-acylglycerol-3-phosph O-acyltransferase 3 0.84 Hs.272062 PTPRF Protein tyrosine phosphatase receptor type F 0.84 Hs.433702 EIF5 Eukaryotic translation initiation factor 5 0.83 Hs.302977 C12orf4 Chromosome 12 open reading frame 4 0.82 Hs.25669 NCOA5 Nuclear receptor coactivator 5 0.79 Hs.356247 ACY1L2 Aminoacylase 1-like 2 0.79 Hs.301277 KIAA0543 KIAA0543 protein 0.79 Hs.524183 FKBP4 FK506 binding protein 4 59kDa 0.76 Hs.461412 - mitochondria: CDNA clone IMAGE:5268125 0.76 Hs.32417 SARG Specifically androgen-regulated protein 0.75 Hs.438545 SLC2A9 Solute carrier family 2, member 9 0.73 Hs.411490 FAM36A Family with sequence similarity 36 member A 0.72 Hs.284491 PDXK Pyridoxal (pyridoxine vitamin B6) kinase 0.68 Hs.302738 SLC26A2 Solute carrier family 26 member 2 0.63 Hs.519452 NPM1 Nucleophosmin 0.61 Hs.533977 TXNIP Thioredoxin interacting protein 0.57 - - Homo sapiens isolate M3 mitochondrion 0.56 Hs.491577 MYST3 MYST histone acetyltransferase 3 0.45 * All p-values < 0.001