Legend to supplemental Figure 1

MMP-9 and MMP-2 activity in plasma from HD, BPH and PCa patients.

Panel A. Zymograms showing gelatinolytic activity in representative plasma. Note the increased intensity of the MMP-9 but not the MMP-2 lower band representative of the active enzyme. Samples were loaded onto 8% polyacrylamide gels co-polymerized with 1 mg/ml gelatin. After electrophoresis, gels were washed three times in 2.5% Triton X-100 at room temperature and incubated overnight at 37° C in 50 mM Tris– HCl, pH 7.5, 200 mM NaCl, 5 mM CaCl2 and 0.02% Brij-35. Gels were stained with 0.5% Coomassie blue (w/v) in 25% methanol (v/v) and 10% acetic acid (v/v), and de-stained in the same solution without Coomassie blue. The supernatant of WM983A melanoma cells, activated or not with p-aminophenylmercuric acetate, was used as a reference standard for human pro-MMP-9, pro-MMP-2 and their activated forms. Plasma samples from HD were used as an internal standard. Panel B. MMP-9 activity quantified by densitometry and expressed as arbitrary units. Box plot shows median and 25th and 75th percentiles (whiskers = minimum and maximum values).

1 Supplemental Figure 1

A

HD BPH BPH BPH PCa PCa PCa PCa

Pro-MMP-9► MMP-9►

Pro-MMP-2 ► MMP-2 ►

B P<0.001 30 20 10 P<0.001 10

8 P>0.05

6 (arbitrary units) MMP-9 activity MMP-9 4

2

0 HD BPHBPH PCaCaP

2 Supplementary Table 1. List of gene sets and genes for GSEA.

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K ACP1 ACTB ACTC1 ACTG1 ACTN1 ACTN2 ACTN3 ACTN4 ACVR1B ACVR1C BAIAP2 CDC42 CDH1 CREBBP CSNK2A1 CSNK2A2 CSNK2B CTNNA1 CTNNA2 CTNNA3 CTNNB1 CTNND1 EGFR EP300 ERBB2 FARP2 FER FGFR1 FKSG30 FYN IGF1R Androgen_Signaling_and_Prostate_Cancer 96 S ACPP ADH1B ADM AKR1B1 ALDH1A1 ANKH APOE ARSDR1 AS3 C7 CDC37 CDH1 CDS1 CHD4 CLU CSNK2B CSTB CYP2C18 DBI DHCR24 DKFZP434 EIF4EBP1 FAT FBXL11 FGF8 FKBP5 FKBP8 FOLH1 FOXJ1 GAGEB1 GAGEC1 Angiogenesis 113 S AKT1 ANGPT1 ANGPT2 ANGPTL3 ANGPTL4 ANPEP BAI1 CCL11 CCL2 CDH5 COL18A1 COL4A3 CSF3 CXCL1 CXCL10 CXCL11 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9 ECGF1 EDG1 EFNA1 EFNA2 EFNA3 EFNA5 EFNB2 EGF ENG EPAS1 Antigen_processing_and_presentation_KEGG 73 K B2M CALR CANX CD4 CD74 CD8A CD8B CIITA CREB1 CTSB CTSL CTSS HLA-A HLA-B HLA-C HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DQB2 HLA-DRA HLA-DRB1 HLA-DRB4 HLA-E HLA-F HLA-G HSP90AA1 Apoptosis 163 S ABL1 AKT1 AKT2 AKT3 APAF1 ATM BAD BAG1 BAG3 BAG4 BAK1 BAX BCL10 BCL2 BCL2A1 BCL2L1 BCL2L10 BCL2L11 BCL2L12 BCL2L13 BCL2L2 BCLAF1 BFAR BID BIK BIRC1 BIRC2 BIRC3 BIRC4 BIRC5 BIRC6 Breast_Cancer_Estrogen_Signaling 101 msigdb SPRR1B PAPPA NME1 ATF2 F3 CTSD CLDN7 TOP2A CTNNB1 MAP2K7 MT3 ITGA6 TFF3 PTGS2 FHL5 MLP PLAU IL6R CCNE1 TP53 ID2 CCNE2 IGFBP2 GATA3 RAC2 CD44 GSN ITGB4 ERBB2 CCNA1 CCND1 Calcium_signaling_pathway_KEGG 171 K ADCY1 ADCY2 ADCY3 ADCY4 ADCY7 ADCY8 ADCY9 ADORA2A ADORA2B ADRA1A ADRA1B ADRA1D ADRB1 ADRB2 ADRB3 AGTR1 ATP2A1 ATP2A2 ATP2A3 ATP2B1 ATP2B2 ATP2B3 ATP2B4 AVPR1A AVPR1B BDKRB2 BST1 CACNA1A CACNA1B CACNA1C CACNA1D Cell_adhesion_molecules_(CAMs)_KEGG 125 K ALCAM CD2 CD22 CD226 CD274 CD276 CD28 CD34 CD4 CD40 CD40LG CD58 CD6 CD80 CD86 CD8A CD8B CD99 CDH1 CDH15 CDH2 CDH3 CDH4 CDH5 CLDN1 CLDN10 CLDN11 CLDN14 CLDN15 CLDN16 CLDN17 Cell_Cycle 89 S CKS1B SFN YWHAQ GSK3B YWHAZ MKI67 PTTG1 RBX1 RBBP8 CKS2 CCND2 GADD45A CHEK1 CDC20 BUB3 CCNA2 CCNB1 CDKN2A RAD17 PLK1 RPA3 MCM4 CDK7 MNAT1 SUMO1 HDAC2 CHEK2 EP300 MCM3 CCNB2 BUB1B Cell_Proliferation 72 Rosenwald et al. TGFA TACSTD2 TNFSF9 KRT16 MET GPC4 EGFR EPHB4 IL1B MYC IL2RG PTHLH IL1A FZD3 EMP2 IL6R SFN ISG20 PDGFA ZFP36L2 EHF TNFRSF9 MIA ARHGEF1 GAB1 NR6A1 TAL1 PIM2 MT3 NDP NUDC Chemokine_Ligand_Receptor 169 S CCL15 CCL3L1 CCL3L3 CCR2 CCR3 CCR5 CCR8 CXCR2 LOC72883 LOC73042BDNF C20orf175 C5 CCBP2 CCL1 CCL1 CCL11 CCL11 CCL12 CCL13 CCL13 CCL14 CCL15 CCL15 CCL16 CCL16 CCL17 CCL17 CCL18 CCL18 CCL19 Colorectal_cancer_KEGG 78 K ACVR1B ACVR1C AKT1 AKT2 AKT3 APC APC2 APPL AXIN1 AXIN2 BAD BAX BCL2 BIRC5 CASP3 CASP9 CCND1 CTNNB1 CYCS DCC DVL1 DVL2 DVL3 EGFR FOS FZD1 FZD10 FZD2 FZD3 FZD4 FZD5 Common_Cytokine 108 S ATP6AP1 BMP10 BMP15 BMP2 BMP3 BMP4 BMP5 BMP6 BMP7 BMP8B CSF1 CSF2 CSF3 CYFIP2 FAM3B FAM3C FASLG FGF10 FLT3LG GDF10 GDF11 GDF15 GDF2 GDF3 GDF5 GDF8 GDF9 IFNA13 IFNA14 IFNA2 IFNA4 Complement_and_coagulation_cascades_KEGG 65 K A2M BDKRB2 C1QA C1QB C1QC C1R C1S C2 C3 C3AR1 C4BPA C4BPB C5 C5AR1 C6 C7 C8A C8B C8G CD46 CD55 CD59 CFB CFD CFH CFI CPB2 CR1 CR2 F10 F11 DNA_Damage_Signaling_Pathway 107 S ANKRD17 ATM ATRX BRCA1 BTG2 CCNH CDK7 CHEK2 CIB1 CIDEA CIDEB CKN1 CRY1 CRY2 DDB1 DDB2 DDIT3 DMC1 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 EXO1 FANCG FEN1 G22P1 GADD45A GADD45G GML GTF2H1 ECM_extracellular 156 S ADIPOQ AGC1 AMELX AMELY BCAN BGN CLU COL10A1 COL11A1 COL11A2 COL12A1 COL13A1 COL14A1 COL15A1 COL16A1 COL17A1 COL18A1 COL19A1 COL1A1 COL1A2 COL20A1 COL21A1 COL22A1 COL23A1 COL24A1 COL25A1 COL27A1 COL2A1 COL3A1 COL4A1 COL4A2 ECM_inhibitors&other_enzymes 82 S AGT APP ChGn CHPF CHST1 CHST10 CHST11 CHST12 CHST13 CHST2 CHST3 CHST4 CHST5 CHST6 CHST7 CHST8 CHST9 CHSY1 CSGlcA-T CSS3 GALNACT- HABP2 HABP4 HAS1 HAS2 HAS3 HYAL1 HYAL2 HYAL3 HYAL4 HYALP1 ECM_membrane_cell-cell_adhesion 138 S ALCAM CDH1 CDH10 CDH11 CDH12 CDH13 CDH15 CDH16 CDH17 CDH18 CDH19 CDH2 CDH20 CDH22 CDH23 CDH24 CDH26 CDH3 CDH4 CDH5 CDH6 CDH7 CDH8 CDH9 CEACAM1 CEACAM19CEACAM21CEACAM3 CEACAM4 CEACAM5 CEACAM6 ECM_membrane_cell-matrix_adhesion 161 S ADRM1 CD164 CD209 CD300A CD36 CD44 CD47 CD6 CD9 CIB1 CIB2 CIB3 CIB4 HMMR ITFG1 ITFG2 ITFG3 ITGA10 ITGA11 ITGA2 ITGA2B ITGA3 ITGA4 ITGA5 ITGA6 ITGA7 ITGA8 ITGA9 ITGAD ITGAE ITGAL ECM_proteases 204 S ACE ACE2 ADAM1 ADAM10 ADAM11 ADAM12 ADAM15 ADAM17 ADAM18 ADAM19 ADAM2 ADAM20 ADAM21 ADAM22 ADAM23 ADAM24 ADAM25 ADAM26 ADAM28 ADAM29 ADAM30 ADAM32 ADAM33 ADAM3A ADAM3B ADAM4 ADAM5 ADAM6 ADAM7 ADAM8 ADAM9 ECM-receptor_interaction_KEGG 85 K AGRIN CD36 CD44 CD47 CHAD COL11A1 COL11A2 COL1A1 COL1A2 COL2A1 COL3A1 COL4A1 COL4A2 COL4A4 COL4A6 COL5A1 COL5A2 COL5A3 COL6A1 COL6A2 COL6A3 DAG1 FN1 FNDC1 FNDC3A FNDC4 FNDC5 GP1BA GP5 GP6 GP9 EGF_PDGF_Signaling_Pathway 96 S ACTR2 ACTR3 AKT1 AKT2 AKT3 ARAF1 ARHA ATF1 ATF2 BAD BCL2 BRAF CASP3 CASP9 CCND1 CHUK COL1A1 CREB1 CSNK2A1 CSNK2B DUSP1 DUSP6 EGF EGFR EGR1 EIF4E ELK1 ENPP2 FN1 FOS FOXO3A Endothelial_Cell_Biology 121 S ABCF1 ACE ACE2 ADAM17 AGT AGTR1 AGTR2 ALOX5 ANGPT1 ANGPT2 ANGPTL3 ANXA5 AZU1 BAX BCL2 BCL2A1 BCL2L1 BCL6 BLR1 C3 C4A CASP1 CASP10 CASP3 CASP6 CCL2 CCL20 CCL5 CDH5 CEBPB CFLAR Focal_adhesion_KEGG 193 K ACTB ACTC1 ACTG1 ACTN1 ACTN2 ACTN3 ACTN4 AKT1 AKT2 AKT3 ARHGAP5 BAD BCAR1 BCL2 BIRC2 BIRC3 BIRC4 BRAF CAPN2 CAV1 CAV2 CAV3 CCND1 CCND2 CCND3 CDC42 CHAD COL11A1 COL11A2 COL1A1 COL1A2 Folate_biosynthesis_KEGG 37 K ALPI ALPL ALPP ALPPL2 ASCC3 ASCC3L1 ATP13A2 DDX18 DDX23 DDX41 DDX47 DDX50 DDX52 DDX54 DDX56 DHFR EP400 ERCC2 ERCC3 FBXO18 FPGS GCH1 GGH IFIH1 LGP2 MOV10L1 NUDT5 NUDT8 PTS QDPR RAD54B G_Protein-Coupled_Receptor 96 S ADORA1 ADORA2A ADORA2B ADORA3 AGTR1 AGTR2 AGTRL1 AVPR1A AVPR1B AVPR2 BDKRB1 BDKRB2 C3AR1 CACNA1D CALCRL CASR CCKAR CCKBR CELSR1 CNR1 CNR2 CRHR1 CRHR2 EBI2 EDG1 EDG2 EDG3 EDG4 EDG6 EDG7 EDG8 G_Protein-Coupled_Receptor_II 97 S ADRA1A ADRA1B ADRA2A ADRA2B ADRA2C ADRB2 ADRB3 ARRB2 BLR1 CCR1 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CHRM1 CHRM2 CHRM3 CHRM4 CHRM5 CMKLR1 CX3CR1 CXCR3 CXCR4 CXCR6 CYSLTR1 DRD1 Gap_junction_KEGG 95 K ADCY1 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRB1 CDC2 CSNK1A1 CSNK1A1L CSNK1D CSNK1E CSNK1G2 CSNK1G3 CX36 DRD1 DRD2 EDG2 EGF EGFR GJA1 GNAI1 GNAI2 GNAI3 GNAQ GNAS GRB2 GRM1 Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. AKR7A3 ANKRD32 ATAD2 BARD1 BRD2 C10orf117 C13orf8 C21orf45 C6orf150 CASP8AP2CCNE1 CCNE2 CDC25A CDC45L CDC6 CDC7 CDCA5 CDCA7 CDT1 CHEK1 CSE1L CSPG5 DCLRE1B DDX10 DIPA DNMT1 EED EGR1 EXOSC6 FEN1 FIGNL1 Genome_Stability_DNA_Repair 113 S ANKRD17 APEX1 APEX2 ATM ATR ATXN3 BRCA1 BRCA2 BRIP1 CCNH CDK7 CETN2 CIB1 CKN1 DDB1 DDB2 DKC1 DMC1 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 EXO1 FEN1 FLJ10858 G22P1 GTF2H1 GTF2H2 GTF2H3 G-Protein_Coupled_Receptors_Signaling 99 S ADRB2 AGTR1 AGTR2 ANGPTL4 ARRB1 ARRB2 BCL2 BCL2L1 CALCR CASR CCND1 CCNE1 CCNE2 CDKN1B CFLAR CMKLR1 COL1A1 CSF3 CTGF CYP19 DRD1 DRD2 DRD5 DUSP14 EDG1 EDG2 EDG3 EDG4 EDG5 EDG7 EGR1 G-Proteins_&_Signaling_Molecules 96 S ADCY1 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY9 AKT1 ARHA ARHGEF1 BRAF BTK CDC42 CHUK CREB1 DTR EGFR EPAC GNA12 GNA13 GNA15 GNAI2 GNAI3 GNAL GNAO1 GNAS1 GNAT1 GNAT2 GNAZ GNB3 GNB4 Growth_Factor 84 S AMH ARTS-1 BDNF BMP1 BMP10 BMP2 BMP3 BMP4 BMP5 BMP6 BMP7 BMP8B CECR1 CLC CSF1 CSF2 CSF3 CSPG5 CXCL1 DKK1 ECGF1 EREG FGF1 FGF11 FGF13 FGF14 FGF17 FGF19 FGF2 FGF22 FGF23 Hedgehog_signaling_pathway_KEGG 55 K BMP2 BMP4 BMP5 BMP6 BMP7 BMP8A BTRC CSNK1A1 CSNK1A1LCSNK1D CSNK1E CSNK1G2 CSNK1G3 DHH FBXW11 GAS1 GLI1 GLI2 GLI3 GSK3B HHIP IHH LRP2 PRKACA PRKACB PRKACG PRKX PRKY PTCH1 PTCH2 RAB23 Hypoxia_Signaling_Pathway 48 S ADD1 ADM AGPAT2 AGTPBP1 ANGPTL4 ARD1 ARNT2 AZU1 BAX BCL2 BHLHB2 BIRC5 CA1 CA12 CA9 CAMK2G CASP1 CAT CDC42 CHGA COL1A1 CREBBP CSTB CTGF CYGB DAPK3 DCTN2 DNAJB1 DR1 ECE1 EEF1A1 IL18_pathway 6 msigdb IL18 IL12B IL2 CASP1 IFNG IL12A IL3_Pathway 15 msigdb RAF1 CSF2RB STAT5A JAK2 SOS1 GRB2 HRAS STAT5B IL3 MAPK3 IL3RA PTPN6 MAP2K1 FOS SHC1 IL6PATHWAY 23 msigdb RAF1 CEBPB PTPN11 SRF JAK2 SOS1 GRB2 HRAS JUN MAPK3 JAK1 IL6ST IL6R JAK3 CSNK2A1 MAP2K1 FOS SHC1 IL6 ELK1 STAT3 IL6PATHWAna IL7PATHWAY 18 msigdb EP300 STAT5A BCL2 STAT5B LCK IL2RG JAK1 JAK3 PIK3CA PIK3R1 IL7R PTK2B IL7 NMI FYN CREBBP IL7PATHWAna Inflammatory_Cytokines_&_Receptors 93 S ABCF1 BCL6 BLR1 C3 C4A C5 CCL1 CCL11 CCL13 CCL15 CCL16 CCL17 CCL18 CCL19 CCL2 CCL20 CCL21 CCL23 CCL24 CCL25 CCL26 CCL3 CCL4 CCL5 CCL7 CCL8 CCR1 CCR2 CCR3 CCR4 CCR5 Inositol_phosphate_metabolism_KEGG 51 K C9orf95 DYRK4 EIF2AK3 FN3K IMPA1 IMPA2 INPP1 INPP4A INPP4B INPP5A INPP5B INPP5E INPPL1 IPMK ISYNA1 ITGB1BP3 ITPKA ITPKB MINPP1 MIOX OCRL PIB5PA PIK3C3 PIK3CA PIK3CB PIK3CD PIK3CG PIK4CA PIK4CB PIP5K1A PIP5K1B Insulin_Signaling_Pathway 171 S ACACA ACACB ACOX1 ADRB3 AEBP1 AHSG AKT1 AKT2 AKT3 ANG ARAF1 BAD BCL2L1 BRAF CALM1 CALM2 CALM3 CALML3 CALML6 CAP1 CBL CBLB CBLC CEBPA CEBPB CEBPD CRK CRKL CSN2 DF DOK1 Interferon 84 S ADAR CNTFR CRLF2 CSF2RA CSF3R CXCL10 EBI3 F3 FNDC6 G1P2 G1P3 IFI16 IFI27 IFI30 IFI35 IFI44 IFI44L IFIH1 IFIT1 IFIT1L IFIT2 IFIT3 IFITM1 IFITM2 IFNA1 IFNA14 IFNA2 IFNA21 IFNA4 IFNA5 IFNA6 Interferon_a,b_Response 96 S ADAR ARL5 ATF5 B2M BAG3 BST2 C1orf29 C6orf85 CASP1 CAV1 CBFB CDKN1B CNP COL16A1 CXCL10 DAD1 DIABLO DNAJB2 FLJ42280 G1P3 GBP1 GBP2 GCH1 GIP2 H19 HLA-A HLA-B HOXB2 HSPA6 IFI16 IFI27 Interleukins_and_Receptors 71 S IL10RB IL11 IL11RA IL12A FIL1 IL10 IL10RA IL12B IL12RB1 IL12RB2 IL13 IL13RA1 IL13RA2 IL14 IL15 IL15RA IL16 IL17 IL17B IL17C IL17E IL17F IL17R IL18 IL18BP IL18R1 IL18RAP IL19 IL1A IL1B IL-1H1 Invasiveness_Gene_Signature 189 Liu et al. CLTC LDHA DNAJB1 PGK1 CIRBP SSR1 COPB2 PLP2 RAD23B PSMA5 SH3BGRL EMP1 SNURF SNRPN ICMT C10ORF7 LTF DPF2 JTV1 MGP GNPDA1 KLF10 NSF MAPK14 STK39 RNF8 HS2ST1 CNOT4 STC2 STAM SRP54 JAK_STAT_Signaling_Pathway 179 S A2M AKT1 AKT2 AKT3 APS BCL2L1 CBL CBLB CBLC CCND1 CCND2 CCND3 CDKN1A CEBPB CISH CLCF1 CNTF CNTFR CREBBP CRK CRKL CRLF2 CRP CSF1R CSF2 CSF2RA CSF2RB CSF3 CSF3R CSN2 CTF1 MAP_Kinase_Signaling_Pathway 97 S AOP2 ARAF1 ATF2 BRAF CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND2 CCND3 CCNE1 CCNE2 CDC42 CDK2 CDK4 CDK6 CDKN1A CDKN1B CDKN1C CDKN2A CDKN2B CDKN2C CHUK COL1A1 CREB1 CREBBP DLK1 DUSP1 E2F1 EGFR Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K ADH1C ADH4 ADH5 ADH6 ADH7 ADHFE1 AKR1C2 AKR1C3 AKR1C4 ALDH1A3 ALDH3A1 ALDH3B1 ALDH3B2 CYP1A1 CYP1A2 CYP1B1 CYP2B6 CYP2C18 CYP2C19 CYP2C8 CYP2C9 CYP2E1 CYP2F1 CYP2S1 CYP3A4 CYP3A43 CYP3A5 CYP3A7 DHDH EPHX1 GSTA1 Metal_Transport_and_Homeostasis 94 S ABCB10 ABCB7 ACO1 ALAS1 ATOX1 ATP7A ATP7B B2M CALR CAT CCS CD163 CP CYBRD1 DIO1 DNAJA1 EGR1 FECH FMO3 FOS FRDA FTH1 FTL GAS1 GPX1 GPX2 GPX3 GPX4 GSR GSS GSTA1 Metalloproteases 34 present_study MMP1 MMP10 MMP11 MMP12 MMP13 MMP14 MMP15 MMP16 MMP17 MMP19 MMP19 /// LMMP2 MMP20 MMP21 MMP23B ///MMP24 MMP25 MMP26 MMP27 MMP28 MMP3 MMP7 MMP8 MMP9 MPP1 MPP2 MPP3 MPP4 MPP5 MPP6 MPP7 Metastasis_adenocarc_dn 34 msigdb CPN1 HR44 KCNAB1 RORB PGK1 ASPA STAC RUNX1 ROR1 MYL2 PCDH11X MYLK CNN1 PBX2 RNASE1 MAOB ACADSB PLP1 CHRNA5 NR4A1 NCAPH ZNF148 P2RX1 INPP5E PTN NR2F2 JMJD1C FXN PDE6A PRKG2 RAB30 Metastasis_adenocarc_up 14 msigdb PRMT1 COL1A1 FBLN2 MAD2L1 PSEN2 STRA13 FASN COL1A2 SNRPF COX7B GPI DHPS P4HB ELF4 mTOR_signaling_pathway_KEGG 49 K AKT1 AKT2 AKT3 BRAF CAB39 DDIT4 EIF4B EIF4E EIF4E2 EIF4EBP1 FIGF FRAP1 GBL HIF1A IGF1 INS KIAA1303 LYK5 MAPK1 MAPK3 PDPK1 PGF PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PRKAA1 Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K BID CASP3 CD244 CD247 CD48 CHP CSF2 FAS FASLG FCER1G FCGR3A FYN GRB2 GZMB HCST HLA-A HLA-B HLA-C HLA-E HLA-G HRAS ICAM1 ICAM2 IFNA1 IFNA10 IFNA13 IFNA14 IFNA16 IFNA17 IFNA2 IFNA21 Neuroscience_Ion_Channels_&_Transporters 104 S ACCN1 ACCN2 ACCN3 APOE ATP1A1 ATP1B1 ATP2A1 ATP2B1 ATP2B4 ATP4A ATP5B ATP6V0A2 ATP6V0D1 ATP6V1A ATP6V1B2 ATP7A ATP7B CACNA1B CACNA1C CACNA1H CACNA1S CACNB1 CACNB2 CACNB3 CACNB4 CACNG2 CETP CFTR CLCA1 CLCN1 CLCN2 Neurotransmitter_Receptors_and_Regulators 107 S ABAT ACHE ANXA9 BAIAP3 BRS3 BZRP CAPON CCKAR CCKBR CHAT CHRM1 CHRM2 CHRM3 CHRNA1 CHRNA2 CHRNA3 CHRNA4 CHRNA5 CHRNA6 CHRNA7 CHRNB1 CHRNB2 CHRNB4 CHRND CHRNE CHRNG COLQ COMT DRD1 DRD2 DRD3 NFkB_Signaling_Pathway 113 S AGT AKT1 APOL3 ATF1 ATF2 BCL10 BCL3 BF BIRC2 C3 CARD10 CARD11 CARD14 CARD4 CASP1 CASP8 CCL2 CFLAR CHUK CSF2 CSF3 CTL2 CXXC5 ECM1 EDARADD EDG2 EGR1 ELK1 F2R FADD FOS Nitric_Oxide 173 S ABCC1 ADM AGTR1 AKT1 ALAS2 ALOX12 APOE ARG2 ATOX1 BCL2 BNIP3 CAMK1 CAT CCL2 CCL3 CCL5 CCNA1 CCS CDKN1A CFTR COL1A1 COL2A1 COL3A1 CSF1 CXCL2 CYBA CYGB CYP19 CYP2D6 CYP3A4 DDAH2 Nitrogen_metabolism_KEGG 24 K AMT ASNS CA1 CA11 CA12 CA13 CA14 CA2 CA3 CA4 CA5A CA5B CA6 CA7 CA8 CA9 CPS1 CTH GLS GLS2 GLUD1 GLUD2 GLUL HAL Notch_Signaling_Pathway 130 S ADAM10 ADAM17 AES APH1A APH-1A AXIN1 CBL CCND1 CCNE1 CD44 CDC16 CDKN1A CDKN1B CFLAR CHUK CIR CREBBP CTBP1 CTBP2 CTNNB1 DLL1 DLL3 DLL4 DTX1 DTX2 DTX3 DTX3L DTX4 DVL1 DVL2 DVL3 Nuclear_Receptors_and_Coregulators 114 S AHR AR ARNT BRD8 C1D CARM1 COPS2 CREBBP CRSP2 CRSP6 DDX5 DMAP1 ERF ESR1 ESR2 ESRRA ESRRB ESRRG HDAC1 HDAC2 HDAC3 HDAC4 HDAC5 HDAC6 HDAC7A HMGA1 HNF4A HNF4G HTATIP ITGB3BP MED12 Oxidative_phosphorylation_KEGG 115 K ATP12A ATP4A ATP4B ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5G2 ATP5G3 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6AP1 ATP6V0A1 ATP6V0A2 ATP6V0A4 ATP6V0B ATP6V0C ATP6V0D1 ATP6V0D2 ATP6V0E ATP6V1A ATP6V1B1 ATP6V1B2 ATP6V1C1 Oxidative_Stress_and_Antioxidant_Defense 84 S ALB ALOX12 ANGPTL7 AOX1 APOE ATOX1 BNIP3 CAT CCL5 CCS CSDE1 CYBA CYGB DGKK DHCR24 DUOX1 DUOX2 DUSP1 EPHX2 EPX FOXM1 GLRX2 GPR156 GPX1 GPX2 GPX3 GPX4 GPX5 GPX6 GPX7 GSR p53_Signaling_Pathway 113 S AATF APAF1 ATM ATR BAG1 BAI1 BAK1 BAP1 BAX BCL2 BCL2A1 BID BIRC5 BNIP3 BRCA1 BRCA2 BTG2 CASP2 CASP9 CCNE2 CCNG2 CCNH CDC2 CDC25A CDC25C CDK4 CDK7 CDKN1A CDKN2A CHEK1 CHEK2 Passerini_Proliferation 65 msigdb TGFB2 CBFA2T2 PDGFRA BAP1 TSHR TSPAN5 EDN1 TOB1 IGFBP7 FSCN1 TIMP1 TUSC2 CLK1 ETS1 BCL2 EGF NUDC CUL1 PRKCA HOXC10 TNFSF4 ARHGEF1 TNFSF11 VHL TACSTD2 CDKN2A ADAMTS8 NF2 IL10 FGFR1OP LAMP3 Phosphatases 105 present_study RPS27A PTPRA PTPRB PTPRC PTPRD PTPRE PTPRF PTPRG PTPRH PTPRJ PTPRK PTPRM PTPRN PTPRN2 PTPRO PTPRQ PTPRR PTPRS PTPRT PTPRU PTPRV PTPRZ1 PTPN1 PTPN2 PTPN3 PTPN4 PTPN5 PTPN6 PTPN7 PTPN9 PTPN11 PI3K-AKT_Signaling_Pathway 113 S ADAR AICDA AKT1 AKT2 AKT3 APC APPL ASAH1 AXIN1 BAD BTK CASP9 CCND1 CD14 CDC42 CDKN1B CHUK CSNK2A1 CTMP CTNNB1 CUTL1 EIF2AK2 EIF3S10 EIF4A1 EIF4B EIF4E EIF4EBP1 EIF4G1 ELK1 FASLG FKBP1A PPAR_signaling_pathway_KEGG 67 K ACAA1 ACADL ACADM ACOX1 ACOX2 ACOX3 ACSL1 ACSL3 ACSL4 ACSL5 ACSL6 ADIPOQ ANGPTL4 APOA1 APOA2 APOA4 APOC3 AQP7 CD36 CPT1A CPT1B CPT1C CPT2 CYP27A1 CYP4A11 CYP7A1 CYP8B1 DBI FABP1 FABP2 FABP3 Proliferation_Signature 51 Whitfield et al. BIRC5 AURKB CDC6 CKS2 TRIP CHEK1 PTTG1 DNMT1 NASP UNG CDC7 FEN1 MCM3 MCM4 MCM5 MCM6 ORC1L PCNA PRIM1 RFC1 RRM1 RRM2 TOP2A MAD2L1 CENPE BUB1 CTPS DHFR TYMS CCNA2 CCNB1 Proteasome_KEGG 31 K PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD6 PSMD7 PSMD8 Recurrence_Score 16 ESR2 PGR BCL2 SCUBE2 MKI67 MYBL2 BIRC5 CCNB1 AURKA ERBB2 GRB7 MMP11 CTSL2 GSTM1 BAG1 CD68 Regulation_of_actin_cytoskeleton_KEGG 201 K ABI2 ACTB ACTC1 ACTG1 ACTN1 ACTN2 ACTN3 ACTN4 APC APC2 ARHGEF1 ARHGEF12 ARHGEF4 ARHGEF6 ARHGEF7 ARPC1A ARPC1B ARPC2 ARPC3 ARPC4 ARPC5 ARPC5L BAIAP2 BCAR1 BDKRB2 BRAF CD14 CDC42 CFL1 CFL2 CHRM1 Regulation_of_autophagy_KEGG 28 K ATG12 ATG3 ATG5 ATG7 BECN1 GABARAP GABARAPLIFNA1 IFNA10 IFNA13 IFNA14 IFNA16 IFNA17 IFNA2 IFNA21 IFNA4 IFNA5 IFNA6 IFNA7 IFNA8 IFNG INS PIK3C3 PIK3R4 PRKAA1 PRKAA2 ULK1 ULK2 Riboflavin_metabolism_KEGG 16 K ACP1 ACP2 ACP5 ACP6 ACPP ACPT ENPP1 ENPP2 ENPP3 FLAD1 MTMR1 MTMR2 MTMR6 PHPT1 RFK TYR Ribosome_KEGG 86 K C15orf15 FAU LOC441907 MRPL13 RPL10 RPL10A RPL10L RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 Rotterdam_signature 68 Jansen et al. PPP1CC ABLIM1 PSMC2 CBX3 /// LOCARHGDIB ZFP36L2 SMC4 PARP4 PLK1 YIF1A TNFSF10 SLC35A1 FKBP2 DUSP4 C11orf9 C11orf51 EEF1A2 MYH2 CNKSR1 FEN1 NEURL CCNE2 GAS2 IL18 MMP23B ///HIST1H4H CAPN2 TNFSF13 //HDGFRP3 CD44 CEP57 Shepard_cell_proliferation 232 msigdb CKS1B CDK6 CBFA2T2 TCF8 CTNNBIP1 C6orf108 ISG20 REGL PDAP2 CDK9 PIM2 VTI1B GPC4 BUB3 CHRM1 MNT CTF1 CRIP1 DD5 ADRA1B RPS4X PDAP1 ZNF187 ERF CDC27 TACSTD2 EVI5 CHRM4 ERG DTYMK SYK Shepard_neg_reg_of_cell_proliferation 116 msigdb DLEC1 TP53I11 CCL23 CD33 RARRES3 SSH3BP1 ATP8A2 SSTR5 IGFBP7 CHEK1 CDC6 MNT MUC12 IL1B TIEG APRIN COL18A1 ADAMTS8 CNOT8 MXD4 CTBP2 EMP3 CTBP1 SSTR4 TM4SF4 HGS HBP17 OSM CDKN2D PMP22 WARS Signal_Transduction_in_Cancer 98 S ATF2 BCL2 BCL2A1 BCL2L1 BIRC1 BIRC2 BIRC3 BMP4 BRCA1 CCND1 cdk4 CDKN1A CDKN1B CDKN1C CDKN2A CDKN2B CDKN2C CDKN2D COL1A1 CSN2 CTSD CXCL9 DUSP1 EDN1 EGFR EGR1 EN1 ENPP2 EPO FN1 FOLH1 Signal_Transduction_Pathway_Finder 114 S A2M ATF2 BAX BCL2 BCL2A1 BCL2L1 BIRC1 BIRC2 BIRC3 BIRC5 BMP2 BMP4 BRCA1 CCL2 CCL20 CCND1 CD5 CDK2 cdk4 CDKN1A CDKN1B CDKN1C CDKN2A CDKN2B CDKN2C CDKN2D CDX1 CEBPB CSF2 CSN2 CTSD Sphingolipid_metabolism_KEGG 37 K ARSA ARSD ARSE ASAH1 B4GALT6 CERK DEGS1 DEGS2 ENPP7 FVT1 GAL3ST1 GALC GBA GLA GLB1 LCT MGC26963NEU1 NEU2 NEU3 NEU4 PHCA PPAP2A PPAP2B PPAP2C SGPL1 SGPP1 SGPP2 SMPD1 SMPD2 SMPD3 Stress_&_Toxicity_Pathway_Finder 96 S ANXA5 ATM BAX BCL2L1 BCL2L2 CASP1 CASP10 CASP8 CCL21 CCL4 CCND1 CCNG1 CHEK2 CRYAB CSF2 CXCL10 CYP1A1 CYP1B1 CYP2E1 CYP7A1 CYP7B1 DDB1 DDIT3 DNAJB4 E2F1 EGR1 EPHX2 ERCC1 ERCC3 ERCC4 ERCC5 Stress_Response_to_Cellular_Damage 96 S ACADSB BAG1 CALR CANX CAT CCT2 CCT3 CCT4 CCT5 CCT7 CCT8 CES1 CLU CRYAA CRYAB CYP11A1 CYP11B2 CYP1A1 CYP1A2 CYP1B1 CYP2A6 CYP2C9 CYP2D6 CYP2E1 CYP2F1 CYP4A11 CYP4B1 CYP7A1 DIA1 DNAJA1 DNAJA2 T_cell_receptor_signaling_pathway_KEGG 92 K AKT1 AKT2 AKT3 BCL10 CARD11 CBL CBLB CBLC CD247 CD28 CD3D CD3E CD3G CD4 CD40LG CD8A CD8B CDC42 CDK4 CHP CHUK CSF2 CTLA4 FOS FYN GRAP2 GRB2 HRAS ICOS IFNG IKBKB T-cell_and_B-cell_Activation 66 S AICDA ANPEP APOA2 AZU1 BLNK BLR1 C1QR1 CCL3 CCL4 CCR1 CCR2 CCR3 CCR4 CCR5 CCR7 CD1D CD2 CD28 CD33 CD3D CD3E CD3G CD4 CD5 CD7 CD80 CD81 CD86 CD8A CD8B1 CLECSF12 TGF-beta_signaling_pathway 116 S ACVR1 ACVR1B ACVR1C ACVR2 ACVR2A ACVR2B ACVRL1 AMH AMHR2 BAMBI BGLAP BMP1 BMP10 BMP15 BMP2 BMP3 BMP4 BMP5 BMP6 BMP7 BMP8A BMP8B BMPER BMPR1A BMPR1B BMPR2 CDC25A CDKN1A CDKN2B CER1 CHRD Th1-Th2-Th3 62 S ATF2 BCL3 CCL11 CCL15 CCL5 CCL7 CCR2 CCR3 CCR4 CCR5 CCR9 CD2 CD28 CD4 CD69 CD80 CD86 CEBPB CREBBP CSF2 CTLA4 CXCR3 FADD FLJ14639 FOS FOSL1 FOSL2 GATA3 GFI1 GLMN GPR44 Tight_junction_KEGG 114 K ACTB ACTC1 ACTG1 ACTN1 ACTN2 ACTN3 ACTN4 AKT1 AKT2 AKT3 AMOTL1 ASH1L CASK CDC42 CDK4 CGN CLDN1 CLDN10 CLDN11 CLDN14 CLDN15 CLDN16 CLDN17 CLDN18 CLDN19 CLDN2 CLDN20 CLDN23 CLDN5 CLDN6 CLDN7 TNF_L&R 28 S LTA LTBR TNF TNFRSF10ATNFRSF10 TNFRSF10 TNFRSF10 TNFRSF11 TNFRSF12 TNFRSF14 TNFRSF19 TNFRSF1A TNFRSF1B TNFRSF21 TNFRSF25 TNFRSF5 TNFRSF6 TNFRSF6BTNFRSF7 TNFRSF9 TNFSF10 TNFSF14 TNFSF18 TNFSF5 TNFSF6 TNFSF7 TNFSF8 TNFSF9 Toll-like_receptor_signaling_pathway_KEGG 90 K AKT1 AKT2 AKT3 ATM CASP8 CCL3 CCL4 CCL5 CD14 CD40 CD80 CD86 CHUK CXCL10 CXCL11 CXCL9 FADD FOS IFNA1 IFNA10 IFNA13 IFNA14 IFNA16 IFNA17 IFNA2 IFNA21 IFNA4 IFNA5 IFNA6 IFNA7 IFNA8 Toxicology_&_Drug_Resistance 73 S ABCB1 ABCB4 ABCC1 ABCC2 ABCC3 ABCC5 ABCC6 ABCG2 ABL1 ACADSB AHR AKT1 AP1S1 APC AR ARNT ATM BAG1 BAX BCL2 BCL2L1 BCL2L2 BCR BRCA1 BRCA2 CALR CANX CASP1 CASP10 CASP8 CAT TSP1_pathway 7 S THBS1 CD36 CASP3 MAPK14 FOS JUN FYN Tumor_Metastasis 59 S HRAS MYC MTSS1 SERPINB5 CTNNB1 IL1B MMP7 PTHLH CAV1 CDKN2A FN1 IL18 MTA1 MMP10 RORB NME1 MTA2 MYCL1 KISS1 CHD4 MET PLAUR EWSR1 RHOC ETV6 HDAC1 DENR CD44 BRMS1 PTP4A3 MMP9 Tumor_Necrosis_Factor 70 S ARHGDIB BAG4 CAD CASP2 CASP3 CASP8 CD40 CD40LG CHUK CRADD DFFA DUSP1 EDA2R FADD FAS FASLG HRB IKBKAP IKBKB IKBKG JUN LMNA LMNB1 LMNB2 LTA LTB LTBR MADD MAP2K4 MAP3K1 MAP3K14 Tumor_Suppressor 26 msigdb MADH4 IRF1 WT1 BRCA2 CDKN2D CCL26 TGFBR1 APC BRCA1 LCMT2 EP300 CDKN1B TSC2 CDKN1C CFL1 TGFBR2 GAPD VHL TP53 MSH2 RB1 NF2 OPN1LW PTEN CREBBP ACTB Tyrosine_metabolism_KEGG 55 K ADH1C ADH4 ADH5 ADH6 ADH7 ADHFE1 ALDH1A3 ALDH3A1 ALDH3B1 ALDH3B2 AOC2 AOC3 AOX1 ARD1A CARM1 COMT DBH DBT DCT DDC ECH1 ESCO1 ESCO2 FAH GOT1 GOT2 GSTZ1 HEMK1 HGD HPD LCMT1 Underhill_proliferation 19 Underhill et al. MCM7 CCNT1 CDK2 MCM4 RECC1 CDC7 RAD17 CDC2L1 CLK2 MCM5 RBL1 CCND1 CDKN2D PA2G4 CHEK2 POLG CCNC GAS5 POLD1 VEGF_signaling_pathway_KEGG 69 K AKT1 AKT2 AKT3 BAD CASP9 CDC42 CHP HRAS HSPB1 HSPB2 KDR KRAS MAP2K1 MAP2K2 MAPK1 MAPK11 MAPK12 MAPK13 MAPK14 MAPK3 MAPKAPK2MAPKAPK3NFAT5 NFATC1 NFATC2 NFATC3 NFATC4 NOS3 NRAS PIK3CA PIK3CB vV_70gene_Signature 61 van't Veer et al. ALDH4A1 AP2B1 AYTL2 BBC3 C16orf61 C20orf46 C9orf30 CCNE2 CDC42BPACDCA7 CENPA COL4A2 DCK DIAPH3 DKFZP686 DTL ECT2 EGLN1 ESM1 EXT1 FBXO31 FGF18 FLT1 GMPS GNAZ GPR126 GPR180 GSTM3 HRASLS IGFBP5 KNTC2 Wnt_Signaling_Pathway 175 S AES APC APC2 AXIN1 AXIN2 BCL9 BTRC CACYBP CAMK2A CAMK2B CAMK2D CAMK2G CCND1 CCND2 CCND3 CER1 CHP CREBBP CSNK1A1 CSNK1A1LCSNK1D CSNK1E CSNK1G1 CSNK1G2 CSNK1G3 CSNK2A1 CSNK2A2 CSNK2B CTBP1 CTBP2 CTNNB1

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 2

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K INSR IQGAP1 LEF1 LMO7 MAP3K7 MAPK1 MAPK3 MET MLLT4 NLK PARD3 PTPN1 PTPN6 PTPRB PTPRF PTPRJ PTPRM PVRL1 PVRL3 PVRL4 RAC1 RAC2 RAC3 RHOA SMAD2 SMAD3 SNAI1 SNAI2 SORBS1 SRC SSX2IP Androgen_Signaling_and_Prostate_Cancer 96 S GPX5 GSTP1 HBOA HMG20B HPN IGF1 IMPDH2 JTB KCNMB1 KLK2 KLK3 KLK4 LDHA LIM MAPKAPK2MDH1 MTA1 MYBL2 NCOA4 NDRG1 NFKBIA NKX3A NR1D1 NSD1 ODC1 OR51E2 PAK6 PART1 PCA3 PCNA PDEF Angiogenesis 113 S EPHB4 EREG F2 FGF1 FGF2 FGF6 FGFR3 FIGF FLT1 HAND2 HGF HIF1A HPSE ID1 ID3 IFNA1 IFNB1 IFNG IGF1 IL10 IL12A IL18 IL1B IL6 IL8 ITGAV ITGB3 JAG1 KDR LAMA5 LECT1 Antigen_processing_and_presentation_KEGG 73 K HSP90AB1 HSPA1A HSPA1B HSPA1L HSPA5 HSPA8 HSPA9B IFI30 IFNA1 IFNA10 IFNA13 IFNA14 IFNA16 IFNA17 IFNA2 IFNA21 IFNA4 IFNA5 IFNA6 IFNA7 IFNA8 KIR2DL1 KIR3DL1 KIR3DL3 KLRC1 KLRC2 KLRC3 KLRC4 KLRD1 LGMN LTA Apoptosis 163 S BIRC7 BIRC8 BNIP1 BNIP2 BNIP3 BNIP3L BOK BRAF CAPN1 CAPN2 CARD10 CARD11 CARD12 CARD14 CARD15 CARD4 CARD6 CARD8 CARD9 CASP1 CASP10 CASP14 CASP2 CASP3 CASP4 CASP5 CASP6 CASP7 CASP8 CASP9 CFLAR Breast_Cancer_Estrogen_Signaling 101 msigdb STC2 PPIA SLC7A5 SCGB1D2 THBS2 CDKN1B C3 CCNA2 TGFA GABRP NFYB TNFSF6 IL6 KLK5 FOSL1 KRT18 DLC1 KRT19 CTSB IL6ST RPL27 FGF1 FLRT1 CYP19A1 NGFR PPP1R15A SERPINE1 CLU IL2RA SCGB2A2 BCL2 Calcium_signaling_pathway_KEGG 171 K CACNA1E CACNA1F CACNA1G CACNA1H CACNA1I CACNA1S CALM1 CALM2 CALM3 CALML3 CALML6 CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CCKAR CCKBR CD38 CHP CHRM1 CHRM2 CHRM3 CHRM5 CHRNA7 CYSLTR1 CYSLTR2 DRD1 EDNRA EDNRB EGFR Cell_adhesion_molecules_(CAMs)_KEGG 125 K CLDN18 CLDN19 CLDN2 CLDN20 CLDN23 CLDN5 CLDN6 CLDN7 CLDN8 CLDN9 CNTN1 CNTN2 CNTNAP1 CNTNAP2 CSPG2 CTLA4 ESAM F11R GLG1 HLA-A HLA-B HLA-C HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DQB2 Cell_Cycle 89 S CDC6 MAD2L1 BIRC5 MCM7 YWHAE CDKN3 SKP2 RAD9A CDC25A YWHAB RAD51 CDC2 MCM5 PCNA E2F2 SMC1A HERC5 CCNA1 MCM2 ESPL1 CDC45L BAX DBF4 TP53 BCCIP ANAPC10 HDAC1 YWHAH RAD50 CDC23 CCNF Cell_Proliferation 72 osenwald et LGI1 PRG4 FGF6 PYY MS4A1 TNFSF8 SKP2 THPO PRL CDK7 FSCN1 TM4SF1 KITLG CDK6 RPS4X HDGF IL3 CKS1B ELF5 PDZK1 PRDX1 MAD1L1 SIPA1 GSPT1 CSF1R TPX2 CKS2 KIF2C RBBP7 HDGFRP3 PDAP1 Chemokine_Ligand_Receptor 169 S CCL19 CCL2 CCL2 CCL20 CCL20 CCL21 CCL21 CCL22 CCL22 CCL23 CCL23 CCL24 CCL24 CCL25 CCL25 CCL26 CCL26 CCL27 CCL27 CCL28 CCL3 CCL3 CCL4 CCL4 CCL4L1 CCL5 CCL5 CCL6 CCL7 CCL7 CCL8 Colorectal_cancer_KEGG 78 K FZD6 FZD7 FZD8 GRB2 GSK3B IGF1R JUN KRAS LEF1 MAP2K1 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 MET MLH1 MSH2 MSH3 MSH6 MYC PDGFRA PDGFRB PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 Common_Cytokine 108 S IFNA5 IFNA8 IFNB1 IFNG IFNK IFNW1 IL10 IL11 IL12A IL12B IL13 IL14 IL15 IL16 IL17 IL17B IL17C IL17E IL17F IL18 IL19 IL1A IL1B IL1F10 IL1F5 IL1F6 IL1F7 IL1F8 IL1F9 IL2 IL20 Complement_and_coagulation_cascades_KEGG 65 K F12 F13A1 F13B F2 F2R F3 F5 F7 F8 F9 FGA FGB FGG KLKB1 KNG1 MASP1 MASP2 MBL2 PLAT PLAU PLAUR PLG PROC PROS1 SERPINA1 SERPINA5 SERPINC1 SERPIND1 SERPINE1 SERPINF2 SERPING1 DNA_Damage_Signaling_Pathway 107 S GTF2H2 GTF2H3 GTSE1 HUS1 IGHMBP2 IHPK3 INPPL1 KUB3 LIG1 LIG3 LIG4 MAP2K6 MAPK12 MBD4 MLH1 MLH3 MNAT1 MPG MRE11A MSH2 MSH3 MSH4 MSH5 MSH6 MUTYH N4BP2 NBS1 NTHL1 NUDT1 OGG1 PCBP4 ECM_extracellular 156 S COL4A3 COL4A3BPCOL4A4 COL4A5 COL4A6 COL5A1 COL5A2 COL5A3 COL6A1 COL6A2 COL6A3 COL7A1 COL8A1 COL8A2 COL9A1 COL9A2 COL9A3 COLQ COMP CSPG2 CSPG3 CSPG4 CSPG4LY CSPG4LYPCSPG4LYPCSPG5 CSPG6 CTHRC1 DAG1 DCN DSPG3 ECM_inhibitors&other_enzymes 82 S MGEA5 SERBP1 SERPINA1 SERPINA10SERPINA12SERPINA2 SERPINA3 SERPINA4 SERPINA5 SERPINA6 SERPINA7 SERPINA9 SERPINB1 SERPINB10SERPINB1 SERPINB12SERPINB13SERPINB2 SERPINB3 SERPINB4 SERPINB5 SERPINB6 SERPINB7 SERPINB8 SERPINB9 SERPINC1 SERPIND1 SERPINE1 SERPINE2 SERPINF1 SERPINF2 ECM_membrane_cell-cell_adhesion 138 S CEACAM7 CEACAM8 CEECAM1 CELSR1 CELSR2 CELSR3 CHL1 DSCAM DSCAML1 FLJ25530 ICAM1 ICAM2 ICAM3 ICAM4 ICAM5 L1CAM LOC402665LOC643998MADCAM1 MCAM MUCDHL NCAM1 NCAM2 NRCAM OPCML PCDH1 PCDH10 PCDH11Y PCDH12 PCDH15 PCDH17 ECM_membrane_cell-matrix_adhesion 161 S ITGAM ITGAV ITGAX ITGB1 ITGB1BP1 ITGB1BP2 ITGB1BP3 ITGB2 ITGB3 ITGB3BP ITGB4 ITGB4BP ITGB5 ITGB6 ITGB7 ITGB8 ITGBL1 LMAN1L MARCO NETO1 NETO2 NRP1 NRP2 NRXN1 NRXN2 NRXN3 PGLYRP1 PGLYRP2 PGLYRP3 PGLYRP4 PIGP ECM_proteases 204 S ADAMDEC ADAMTS1 ADAMTS10ADAMTS11ADAMTS12ADAMTS13ADAMTS14ADAMTS15ADAMTS16ADAMTS17ADAMTS18ADAMTS19ADAMTS2 ADAMTS20ADAMTS21ADAMTS3 ADAMTS4 ADAMTS5 ADAMTS6 ADAMTS7 ADAMTS8 ADAMTS9 ADAMTSL1ADAMTSL2ADAMTSL3ADAMTSL4ADAMTSL5CORIN CPA3 CPD CPE ECM-receptor_interaction_KEGG 85 K HMMR HSPG2 IBSP ITGA10 ITGA11 ITGA2 ITGA2B ITGA3 ITGA4 ITGA5 ITGA6 ITGA7 ITGA8 ITGA9 ITGAV ITGB1 ITGB3 ITGB4 ITGB5 ITGB6 ITGB7 ITGB8 LAMA1 LAMA2 LAMA3 LAMA4 LAMA5 LAMB1 LAMB2 LAMB3 LAMB4 EGF_PDGF_Signaling_Pathway 96 S GAB1 GRB2 GSK3A GSK3B HRAS HSPA5 HSPCA HSPCB ICAM1 IGFBP1 IKBKB IL2 INPP5D JAK1 JUN KRAS2 LTA MAP2K1 MAP2K4 MAP2K7 MAP3K1 MAP3K2 MAP3K3 MAP3K8 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 MKNK1 MKNK2 Endothelial_Cell_Biology 121 S CHGA COL18A1 CPB2 CRADD CRP CSF2 CSF3 CX3CL1 ECGF1 EDG3 EDN1 EDN2 EDN3 EDNRA EDNRB ENPEP F3 FGF1 FGF2 FLT1 FLT3 FLT4 FN1 ICAM1 ICAM2 ICAM3 ICEBERG IFNB1 IL11 IL14 IL15 Focal_adhesion_KEGG 193 K COL2A1 COL3A1 COL4A1 COL4A2 COL4A4 COL4A6 COL5A1 COL5A2 COL5A3 COL6A1 COL6A2 COL6A3 COMP CRK CRKL CTNNB1 DIAPH1 DOCK1 EGF EGFR ELK1 ERBB2 FARP2 FIGF FKSG30 FLNA FLNB FLNC FLT1 FN1 FYN Folate_biosynthesis_KEGG 37 K RAD54L RUVBL2 SETX SMARCA2 SMARCA5 SPR G_Protein-Coupled_Receptor 96 S EDNRA EDNRB F2R F2RL1 F2RL2 F2RL3 FPR1 FPRL1 G2A GCGR GHSR GIPR GLP2R GPR23 GPR68 GRB2 GRM1 GRM2 GRM3 GRM4 GRM5 GRM6 GRM7 GRM8 HRH1 HRH2 HRH3 LHCGR LTB4R LTB4R2 MC1R G_Protein-Coupled_Receptor_II 97 S DRD2 DRD3 DRD5 DRIP78 EBF GABRR2 GPR145 GPR31 GPR44 GPR74 GPRK2L GPRK5 GPRK6 HM74 HTR1A HTR1B HTR1D HTR1E HTR1F HTR2A HTR2B HTR2C HTR3A HTR4 HTR5A HTR7 IL8RA IL8RB KISS1 LPXN MAP2K4 Gap_junction_KEGG 95 K GRM5 GUCY1A2 GUCY1A3 GUCY1B2 GUCY1B3 GUCY2C GUCY2D GUCY2F HRAS HTR2A HTR2B HTR2C ITPR1 ITPR2 ITPR3 K-ALPHA-1KRAS MAP2K1 MAP2K2 MAP2K5 MAP3K2 MAPK1 MAPK3 MAPK7 NPR1 NPR2 NRAS PDGFB PDGFC PDGFD PDGFRA Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. FLJ10719 FLJ11078 FLJ12973 FLJ13912 FLJ20257 FLJ20516 FLJ34077 GADD45B GAL GAS2L1 GEMIN4 GMNN GPR27 H2AFX HSPA1A HSPA1B ID1 IER2 IL17D IL17RB ITPKC JPH1 JUN JUNB KCTD12 KIAA0153 KIAA0186 KIAA0406 KIAA1393 LEF1 LMNB1 Genome_Stability_DNA_Repair 113 S GTF2H4 KUB3 LIG1 LIG3 LIG4 MBD4 MGMT MLH1 MLH3 MMS19L MNAT1 MPG MRE11A MSH2 MSH3 MSH4 MSH5 MSH6 MUTYH N4BP2 NBS1 NEIL1 NEIL2 NTHL1 OGG1 PARP1 PARP3 PINX1 PMS1 PMS2 PMS2L1 G-Protein_Coupled_Receptors_Signaling 99 S ELK1 ELK4 F3 FGF2 FLJ10210 FOS GNAQ GNAS GNRH1 GRM2 GRM4 GRM7 GRM8 HM74 HSD3B1 HSPA4 HSPCA ICAM1 IL1B IL1R1 IL1R2 IL2 IL4 IL6 IL8 JUN JUNB LHB LHCGR LOC116071MAX G-Proteins_&_Signaling_Molecules 96 S GNB5 GNG10 GNG11 GNG12 GNG2 GNG3 GNG4 GNG7 GNGT1 GNGT2 GRB2 HRAS JUN KRAS2 MAP2K1 MAP2K2 MAP2K4 MAP2K5 MAP3K5 MAPK1 MAPK3 MAPK7 MAPK8 MEF2A NFKB1 NFKBIA NRAS PDE1A PDE1B PDE4B PDPK1 Growth_Factor 84 S FGF5 FGF6 FGF7 FGF9 FIGF GDF10 GDF11 GDF8 GDNF GPI HBEGF IGF1 IGF2 IL10 IL11 IL12B IL18 IL1A IL1B IL2 IL3 IL4 INHA INHBA INHBB JAG1 JAG2 LEFTY1 LEFTY2 LIF LTBP4 Hedgehog_signaling_pathway_KEGG 55 K SHH SMO STK36 SUFU WNT1 WNT10A WNT10B WNT11 WNT16 WNT2 WNT2B WNT3 WNT3A WNT4 WNT5A WNT5B WNT6 WNT7A WNT7B WNT8A WNT8B WNT9A WNT9B ZIC2 Hypoxia_Signaling_Pathway 48 S EGFR EGLN2 ENO1 EP300 EPAS1 EPO FNBP3 FOS GAP43 GNA11 GPI GPX1 GSTO1 HBB HIF1A HIF1AN HIF3A IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S CCR6 CCR7 CCR8 CCR9 CEBPB CRP CX3CL1 CX3CR1 CXCL1 CXCL10 CXCL11 CXCL12 CXCL13 CXCL14 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9 CXCR4 EDG3 ICEBERG IFNA2 IFNG IL10 IL10RA IL10RB IL11 IL11RA IL12A IL12B Inositol_phosphate_metabolism_KEGG 51 K PIP5K1C PIP5K2A PIP5K2B PIP5K2C PIP5K3 PLCB1 PLCB2 PLCB3 PLCB4 PLCD1 PLCD3 PLCD4 PLCE1 PLCG1 PLCG2 PLCZ1 PTEN SKIP SYNJ1 SYNJ2 Insulin_Signaling_Pathway 171 S DOK2 DOK3 DOK4 DOK5 DOK6 DUSP14 EIF2B1 EIF4E EIF4E2 EIF4EBP1 ELK1 ERCC1 EXOC7 FASN FBP1 FBP2 FLOT1 FLOT2 FOS FOXO1A FRAP1 FRS2 FRS3 G6PC G6PD GAB1 GCG GCK GPD1 GPD2 GRB10 Interferon 84 S IFNA8 IFNAR1 IFNAR2 IFNB1 IFNE1 IFNG IFNGR1 IFNGR2 IFNK IFNW1 IFRD1 IFRD2 IL10RA IL10RB IL11RA IL12B IL13RA1 IL15 IL20RA IL21R IL22RA2 IL28A IL28RA IL29 IL2RB IL2RG IL31RA IL3RA IL4R IL5RA IL6 Interferon_a,b_Response 96 S IFI30 IFI35 IFI44 IFIT1 IFIT2 IFIT4 IFIT5 IFITM1 IFITM2 IFNA1 IFNAR1 IFNAR2 IFNB1 IFNG IFNW1 IFRD1 IFRD2 IL2RB IRF1 IRF2 IRF3 IRF5 IRF7 ISG20 ISGF3G ITIH2 JAK1 KIAA1268 KLK3 LAMP1 MAL Interleukins_and_Receptors 71 S IL1HY1 IL1R2 IL1RAP IL1RAPL1 IL1RAPL2 IL1RL1 IL1RL2 IL1RN IL2 IL20 IL20RA IL21 IL21R IL22 IL22R IL22RA2 IL23A IL24 IL26 IL2RA IL2RB IL2RG IL3 IL3RA IL4 IL4R IL5 IL5RA IL6 IL6R IL6ST Invasiveness_Gene_Signature 189 Liu et al. BCL2 ELP4 RNF31 ISGF3G WFDC2 MAPT CEBPD KLHL20 MMP7 THEM2 MLF1 PEBP1 ZBTB20 ATXN3 SCGN KDELR3 METTL7A ECOP NDEL1 PRSS16 FLNB VIL2 ATIC GOLGA8A REEP5 PAK2 C1ORF63 SWAP70 EIF4E2 PLAA CXCL2 JAK_STAT_Signaling_Pathway 179 S CXCL9 EGFR EP300 EPO EPOR F2 F2R FCER1A FCER2 FCGR1A G1P2 G1P3 GATA3 GBP1 GHR GRB2 HMGA1 IFNA1 IFNA10 IFNA13 IFNA14 IFNA16 IFNA17 IFNA2 IFNA21 IFNA4 IFNA5 IFNA6 IFNA7 IFNA8 IFNAR1 MAP_Kinase_Signaling_Pathway 97 S EGR1 ELK1 ELK4 ENPP2 ETS1 ETS2 FOS GRB2 HRAS HSPA5 HSPB1 JNKK1) JUN KRAS2 KSR MADH4 MAP2K1 MAP2K1IP1MAP2K2 MAP2K3 MAP2K4 MAP2K5 MAP2K6 MAP2K7 MAP3K1 MAP3K11 MAP3K14 MAP3K2 MAP3K3 MAP3K4 MAP3K5 Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K GSTA2 GSTA3 GSTA4 GSTA5 GSTK1 GSTM1 GSTM2 GSTM3 GSTM4 GSTM5 GSTO1 GSTO2 GSTP1 GSTT1 GSTT2 GSTZ1 MGST1 MGST2 MGST3 UGT1A6 UGT2A1 UGT2B10 UGT2B11 UGT2B15 UGT2B17 UGT2B28 UGT2B4 UGT2B7 Metal_Transport_and_Homeostasis 94 S HAMP HD HEPH HFE HIF1A HMOX1 HMOX2 HP HPX HSPA1A HSPA5 HSPA9B HSPB1 HSPD1 HSPH1 IREB2 JUN LOX LTF MFI2 MPO MT2A MT3 MTF1 MYC NOS1 PMP22 POPDC2 POR PRDX4 SELM Metalloproteases 34 resent_stud MPPE1 MPPED1 MPPED2 Metastasis_adenocarc_dn 34 msigdb RBM5 ABLIM1 DLG3 Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K PRKAA2 RHEB RICTOR RPS6 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA6 RPS6KB1 RPS6KB2 STK11 TSC1 TSC2 ULK1 ULK2 VEGF VEGFB VEGFC Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K IFNA4 IFNA5 IFNA6 IFNA7 IFNA8 IFNAR1 IFNAR2 IFNB1 IFNG IFNGR1 IFNGR2 ITGAL ITGB2 KIR2DL1 KIR3DL1 KLRC1 KLRC2 KLRC3 KLRD1 KRAS LAT LCK LCP2 MAP2K1 MAP2K2 MAPK1 MAPK3 MICA MICB NCR1 NCR2 Neuroscience_Ion_Channels_&_Transporters 104 S CLCN3 CLCN4 CLCN5 CLCN6 CLCN7 CLIC1 CLIC2 KCNA1 KCNA2 KCNA3 KCNA4 KCNA5 KCNB1 KCNB2 KCNC1 KCNC4 KCND1 KCND2 KCNE1 KCNF1 KCNG1 KCNH1 KCNH2 KCNJ1 KCNJ11 KCNJ3 KCNJ4 KCNJ5 KCNJ6 KCNMB1 KCNN1 Neurotransmitter_Receptors_and_Regulators 107 S GABRA1 GABRA2 GABRA3 GABRB1 GABRB2 GABRD GABRE GABRG1 GABRG2 GABRP GABRQ GABRR2 GAD1 GAD2 GALR1 GALR2 GALR3 GCH1 GCHFR GLRA1 GLRA2 GLRA3 GPR10 GPR103 GPR147 GPR24 GPR73 GPR73L1 GPR74 GPR83 GRIA1 NFkB_Signaling_Pathway 113 S GJA1 GPR89 HMOX1 HNLF HTR2B ICAM1 IFNA1 IFNB1 IFNG IKBKB IKBKE IKBKG IL10 IL1A IL1B IL1R1 IL6 IL8 IRAK1 IRAK2 JUN LITAF LTA LTBR MALT1 MAP2K3 MAP2K4 MAP2K6 MAP3K1 MAP3K14 MAP3K3 Nitric_Oxide 173 S DDIT3 DLG4 DNCL1 DUOX1 DUOX2 DUSP1 EDN1 EDNRB EGFR EGR1 EPO EPX FLJ37174 FLT1 FMR1 FN1 FOXM1 FTL GADD45A GADD45B GCH1 GCHFR GCLC GCLM GLA GLRX2 GPR156 GPX1 GPX2 GPX3 GPX4 Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S EP300 FIGF FOS FOSL1 FZD1 FZD10 FZD2 FZD3 FZD4 FZD6 FZD7 FZD8 FZD9 GBP2 GCN5L2 GLI1 GLI2 GLI3 GSK3B HDAC1 HDAC2 HES1 HES5 HES6 HEY1 HEY2 HEYL HOXB4 HR IFNG IL17B Nuclear_Receptors_and_Coregulators 114 S MED4 MLR2 MTA1 MYST4 NCOA1 NCOA2 NCOA3 NCOA4 NCOA6 NCOA6IP NCOR1 NCOR2 NFKB2 NONO NOTCH2 NPM1 NR0B1 NR0B2 NR1D1 NR1D2 NR1H2 NR1H3 NR1H4 NR1I2 NR1I3 NR2C1 NR2C2 NR2E1 NR2E3 NR2F1 NR2F2 Oxidative_phosphorylation_KEGG 115 K ATP6V1C2 ATP6V1D ATP6V1E1 ATP6V1E2 ATP6V1F ATP6V1G1 ATP6V1G2 ATP6V1G3 ATP6V1H COX10 COX11 COX15 COX17 COX4I1 COX4I2 COX5A COX5B COX6A1 COX6A2 COX6B1 COX6B2 COX6C COX7A1 COX7A2 COX7A2L COX7B COX7B2 COX7C COX8A CYC1 NDUFA1 Oxidative_Stress_and_Antioxidant_Defense 84 S GSS GSTZ1 GTF2I KRT1 LPO MBL2 MGST3 MPO MPV17 MSRA MT3 MTL5 NCF1 NCF2 NME5 NOS2A NOX5 NUDT1 OXR1 OXSR1 PDLIM1 PIP3-E PNKP PRDX1 PRDX2 PRDX3 PRDX4 PRDX5 PRDX6 PREX1 PRG3 p53_Signaling_Pathway 113 S CIAO1 COPEB CRADD CYR61 DAPK1 DAXX E2F1 E2F3 EI24 ESR1 FADD FAF1 FOXO3A FRAP1 GADD45A GAK GAS1 GML GTSE1 HDAC1 HK2 IFNB1 IGF1R IL6 JUN KRAS2 LRDD MCL1 MDM2 MDM4 MSH2 Passerini_Proliferation 65 msigdb IL8RB USP8 SPOCK1 CUL4A IL1A FGF2 CDC25C CXCL10 MAPRE1 FLT1 UBE2V2 PMP22 PRKRA MAD1L1 CDKN2C CDKN1B PLG IL12RB1 CDKN1C HBEGF PCNA KLF4 VEGFC NULL TGFA PBEF1 PGF PTK2B EMP1 E4F1 CDKN1A Phosphatases 105 resent_stud PTPN12 PTPN13 PTPN14 PTPN18 PTPN20B PTPN21 PTPN22 PTPN23 DUSP1 DUSP2 DUSP4 DUSP5 DUSP6 DUSP7 DUSP8 DUSP9 DUSP10 DUSP16 STYXL1 DUSP3 DUSP11 DUSP12 DUSP13 DUSP14 DUSP15 DUSP18 DUSP19 DUSP21 DUSP22 DUSP23 DUSP26 PI3K-AKT_Signaling_Pathway 113 S FOS FOXO1A FOXO3A FRAP1 FZD1 GHR GJA1 GNB1 GRB10 GRB2 GSK3B HRAS HSPB1 HSPCA HSPCB IGF1 IGF1R ILK INPP5D INPPL1 IRAK1 IRS1 ITGB1 JUN LBP LEF1 LY96 MAP2K1 MAPK1 MAPK14 MAPK3 PPAR_signaling_pathway_KEGG 67 K FABP4 FABP5 FABP6 FABP7 FADS2 GK GK2 HMGCS1 HSD17B4 ILK LPL ME1 MMP1 NR1H3 OLR1 PCK1 PCK2 PDPK1 PLIN PLTP PPARA PPARD PPARG RXRA RXRB RXRG SCD SCP2 SLC27A1 SLC27A2 SLC27A4 Proliferation_Signature 51 Whitfield et a CCNE1 CCNF CDC20 DDX11 E2F3 MKI67 PKMYT1 PLK1 TIMP1 CDC25C CENPF MAPK13 EXOSC9 MYB TP53 CDH3 EGFR ERBB2 CCNE2 KRT5 Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K CHRM2 CHRM3 CHRM4 CHRM5 CRK CRKL CSK CYFIP1 CYFIP2 DIAPH1 DIAPH2 DIAPH3 DOCK1 EGF EGFR F2 F2R FGD1 FGD3 FGF1 FGF10 FGF11 FGF12 FGF13 FGF14 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL36AL RPL37 RPL37A RPL38 RPL39 RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPLP0 RPLP1 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 Rotterdam_signature 68 Jansen et al ORC3L SAT1 GTSE1 TACC2 KPNA2 /// LAP2A2 MAP4 BICD1 FLJ25476 EIF4EBP3 /ETV2 LST1 FUT3 MAG COL2A1 LOC653879GOLPH2 SUPT16H RFXDC2 ZCCHC8 UCKL1 ATAD2 MLF1IP C1orf66 CLN8 POLQ NCAPG2 KIAA0748 GABRQ GFOD2 BCL2L14 Shepard_cell_proliferation 232 msigdb CYR61 TXN OSMR MS4A1 EMP3 CHRM5 USP8 INSL4 IL2RG TCF19 IL9R PDCD1LG1SKB1 BTG1 KHDRBS1 RPP14 BST2 BUB1 UHRF1 RPS27 SIPA1 TGFA ELN TRIP EMP1 SPOCK TGFB2 CKS2 MET ELF5 PYY Shepard_neg_reg_of_cell_proliferation 116 msigdb ADRA1A BTG1 CDKN1B IL8 CDKN1C APEG1 CDK10 CGREF1 LDOC1 GNRH1 PTHLH IL6 PPM1D QSCN6 DLG5 PRKR BTG2 S100A11 BAP1 FRK BTG3 39783 TOB1 GML FABP7 TGFB1I1 CDKN3 SSTR2 ETS1 MXI1 ZRANB1 Signal_Transduction_in_Cancer 98 S FOS FOSL1 FOXA2 GADD45A HHIP HIF1A HK1 HMOX1 HSPA4 HSPA5 HSPB1 HSPB2 HSPCA ID2 IGFBP3 IL2 IL4 IL4R IRF1 JUN KLK2 KLK3 LTA MCL1 MDM2 MMP10 MMP7 MYC NFKB1 NFKBIA NOS2A Signal_Transduction_Pathway_Finder 114 S CXCL12 CXCL9 CYP19A1 EGFR EGR1 EN1 FASN FLJ12541 FN1 FOS FOXA2 GADD45A GREB1 GYS1 HHIP HK2 HOXA1 HOXB1 HSF1 HSPB1 HSPCA ICAM1 IGFBP3 IGFBP4 IKBKB IL1A IL2 IL2RA IL4 IL4R IL8 Sphingolipid_metabolism_KEGG 37 K SPHK1 SPTLC1 SPTLC2 TMEM23 UGCG UGT8 Stress_&_Toxicity_Pathway_Finder 96 S FMO1 FMO5 GADD45A GADD45B GDF15 GPX1 GSR GSTM3 HMOX1 HMOX2 HSF1 HSPA1A HSPA1L HSPA2 HSPA4 HSPA5 HSPA6 HSPA8 HSPA9B HSPB1 HSPCA HSPCB HSPD1 HSPE1 HSPH1 IGFBP6 IL18 IL1A IL1B IL6 LTA Stress_Response_to_Cellular_Damage 96 S DNAJA3 DNAJA4 DNAJB1 DNAJB11 DNAJB2 DNAJB4 DNAJB5 DNAJB6 DNAJB9 DNAJC4 DNAJC5 DNAJC6 DNAJC7 DNAJC8 DNAJC9 DNAJD1 EPHX2 FMO1 FMO4 FMO5 GPX1 GPX2 GRP58 GSR GSTM3 GSTO1 GSTP1 GSTT1 HMOX1 HMOX2 HOP T_cell_receptor_signaling_pathway_KEGG 92 K IKBKG IL10 IL2 IL4 IL5 ITK JUN KRAS LAT LCK LCP2 MALT1 MAP3K14 MAP3K8 NCK1 NCK2 NFAT5 NFATC1 NFATC2 NFATC3 NFATC4 NFKB1 NFKB2 NFKBIA NFKBIB NFKBIE NRAS PAK1 PAK2 PAK3 PAK4 T-cell_and_B-cell_Activation 66 S CSF2 CX3CL1 CXCR3 CXCR4 GALNAC4SGLMN HDAC4 HDAC5 HDAC7A HDAC9 HLA-DRA ICOSL IFNA2 IFNB1 IFNG IFNGR1 IFNGR2 IFNK IGBP1 IL10 IL11 IL12A IL12B IL12RB1 IL12RB2 IL13 IL18 IL18R1 IL2 IL21R IL27 TGF-beta_signaling_pathway 116 S COL1A1 COL1A2 COL3A1 COMP CREBBP CST3 CUL1 DCN DLX2 E2F4 E2F5 ENG EP300 EVI1 FKBP1B FOS FST GDF1 GDF10 GDF11 GDF15 GDF2 GDF3 GDF5 GDF6 GDF7 GDF8 GDF9 GREM1 GSC HIPK2 Th1-Th2-Th3 62 S HAVCR2 ICOS IFNG IGSF6 IL10 IL12B IL12RB2 IL13 IL13RA1 IL13RA2 IL15 IL17F IL18 IL18BP IL18R1 IL1R1 IL1R2 IL2 IL27 IL2RA IL4 IL4R IL5 IL6 IL6R IL7 IL9 INHA INHBA IRF1 IRF4 Tight_junction_KEGG 114 K CLDN8 CLDN9 CRB3 CSDA CSNK2A1 CSNK2A2 CSNK2B CTNNA1 CTNNA2 CTNNA3 CTNNB1 CTTN EPB41 EPB41L1 EPB41L2 EPB41L3 EXOC3 EXOC4 F11R FKSG30 GNAI1 GNAI2 GNAI3 HCLS1 HRAS INADL JAM2 JAM3 KRAS LLGL1 LLGL2 TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K IFNAR1 IFNAR2 IFNB1 IKBKB IKBKE IKBKG IL12A IL12B IL1B IL6 IL8 IRAK1 IRAK4 IRF3 JUN LBP LY96 MAP2K3 MAP2K4 MAP2K6 MAP3K7 MAP3K7IP1MAP3K7IP2MAPK10 MAPK11 MAPK12 MAPK13 MAPK14 MAPK8 MAPK9 MYD88 Toxicology_&_Drug_Resistance 73 S CCL21 CCL3 CCL4 CCNC CCND1 CCNE1 CCNG1 CCT2 CCT3 CCT4 CCT5 CCT7 CCT8 CDK2 CDK4 CDKN1A CDKN1B CDKN2A CDKN2D CES1 CHEK2 CHST1 CHST10 CHST2 CHST3 CHST4 CHST5 CHST6 CHST7 CHST8 CLU TSP1_pathway 7 S Tumor_Metastasis 59 S BAI1 GNRH2 METAP2 RB1 FGFR4 IL8RB MDM2 MYB FLT4 CDK4 ITGA7 PCOLN3 ETV4 S100A4 CXCL12 HPSE GNRH1 GZMA NME4 NF2 CXCR4 MMP13 APC NR4A3 CST7 MMP11 HTATIP2 CTNNA1 Tumor_Necrosis_Factor 70 S MAP3K7 MAPK8 NFKB1 NFKBIA NGFR PAK1 PAK2 PARP1 PGLYRP1 PRKDC RB1 SPTAN1 TANK TNF TNFAIP3 TNFRSF10 TNFRSF10 TNFRSF10 TNFRSF10 TNFRSF11 TNFRSF11 TNFRSF12 TNFRSF13 TNFRSF13 TNFRSF14 TNFRSF17 TNFRSF18 TNFRSF19 TNFRSF19 TNFRSF1ATNFRSF1B Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K LCMT2 MAOA MAOB METTL2B METTL6 MIF MYST3 MYST4 NAT5 PNMT PNPLA3 PRMT1 PRMT2 PRMT3 PRMT5 PRMT6 PRMT7 PRMT8 SH3GLB1 TAT TH TPO TYR TYRP1 Underhill_proliferation 19 nderhill et al. VEGF_signaling_pathway_KEGG 69 K PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PLA2G10 PLA2G12A PLA2G12B PLA2G1B PLA2G2A PLA2G2D PLA2G2E PLA2G2F PLA2G3 PLA2G4A PLA2G5 PLA2G6 PLCG1 PLCG2 PPP3CA PPP3CB PPP3CC PPP3R1 PRKCA PRKCB1 PRKCG PTK2 PXN RAC1 RAC2 vV_70gene_Signature 61 an't Veer et aLGP2 LOC643008MCM6 MELK MMP9 MS4A7 MTDH NMU NUSAP1 ORC6L OXCT1 PALM2-AKAPECI PITRM1 PQLC2 PRC1 QSCN6L1 RAB6A RFC4 RP5-860F1RTN4RL1 RUNDC1 SCUBE2 SLC2A14 STK32B TGFB3 TSPYL5 UCHL5 WISP1 ZNF533 Wnt_Signaling_Pathway 175 S CTNNBIP1 CUL1 CXXC4 DAAM1 DAAM2 DIXDC1 DKK1 DKK2 DKK3 DKK4 DVL1 DVL2 DVL3 EP300 FBXW11 FBXW2 FGF4 FOSL1 FOXN1 FRAT1 FRAT2 FRZB FSHB FZD1 FZD10 FZD2 FZD3 FZD4 FZD5 FZD6 FZD7 NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG,S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013- 21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 3

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 TCF7 K TCF7L1 TCF7L2 TGFBR1 TGFBR2 TJP1 VCL WAS WASF1 WASF2 WASF3 WASL YES1 Androgen_Signaling_and_Prostate_Cancer 96 PIG8 S PPAP2A PPAP2B PSCA PTEN RAN RAP1A RNF14 RPA3 SFRP4 SHBG SPARCL1 SRD5A2 SREBF1 SREBF2 STEAP TGFB1I 1 TGM4 TMEPAI TMF1 TMPRSS2 TNFRSF6 TRIM28 TUBA3 XRCC2 ADAM9 AIG-1 ANXA7 AR BCRP1 C20orf1 Angiogenesis 113 LEP S MDK MMP19 MMP2 MMP9 NOTCH4 NPPB NPR1 NRP1 NRP2 NUDT6 PDGFA PDGFB PECAM1 PF4 PGF PLAU PLG PLXDC1 PROK2 PTEN PTGS1 PTGS2 PTN RNASE4 SERPINF1 SH2D2A SPHK1 STAB1 STAB2 TEK Antigen_processing_and_presentation_KEGG 73 NFYA K NFYB NFYC PDIA3 PSME1 PSME2 RFX5 RFXAP TAP1 TAP2 TAPBP Apoptosis 163 CHP S CHUK CIDEA CIDEB CRADD CSF2RB CYCS DAPK1 DAPK2 DFFA DFFB ENDOG FADD FAS FASLG GADD45A GDNF HRK IGF1R IKBKB IKBKG IL1A IL1B IL1R1 IL1RAP IL3 IL3RA IRAK1 IRAK2 IRAK4 LTA Breast_Cancer_Estrogen_Signaling 101 HSPB1 msigdb HMGB1 SCGB2A1 MUC1 TNFAIP2 VEGF TFF1 MKI67 CDKN2A TNFRSF6 TIE AZGP1 ESR1 EGFR ESR2 JUN RPL13A S100A2 KLF5 BPAG1 SERPINA3 NGFB KRTHB6 KIT SERPINB5 PGR AR GAPD THBS1 CDH1 THBS4 Calcium_signaling_pathway_KEGG 171 ERBB2 K ERBB3 ERBB4 F2R GNA14 GNAL GNAQ GNAS GRIN1 GRIN2A GRIN2C GRIN2D GRM1 GRM5 GRPR HRH1 HRH2 HTR2A HTR2B HTR2C HTR4 HTR5A HTR6 HTR7 ITPKA ITPKB ITPR1 ITPR2 ITPR3 LHCGR MLCK Cell_adhesion_molecules_(CAMs)_KEGG 125 HLA-DRA K HLA-DRB1 HLA-DRB4 HLA-E HLA-F HLA-G ICAM1 ICAM2 ICAM3 ICOS ICOSLG IGSF4 IGSF4B ITGA4 ITGA6 ITGA8 ITGA9 ITGAL ITGAM ITGAV ITGB1 ITGB2 ITGB7 ITGB8 JAM2 JAM3 L1CAM MADCAM1 MAG MPZ MPZL1 Cell_Cycle 89 CDC7 S SKP1A MCM6 CDK5RAP1BCL2 CDC34 CDK6 GTSE1 CCNT1 MAD1L1 CDKN2B CDK5R2 ORC6L CUL2 CDK8 BUB1 CCNH E2F1 TFDP1 DDX11 CCNG2 ATR ORC2L CUL1 CDC25C ANAPC5 RB1 Cell_Proliferation 72 BUB1B Rosenwald et al. BUB1 EVI5 BUB3 PCNA IL6 MNAT1 MTCP1 KHDRBS1 TFDP1 Chemokine_Ligand_Receptor 169 CCL8 S CCL9/10 CCR1CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CCRL2 CKLF CKLFSF1 CKLFSF2 CKLFSF3 CKLFSF4 CKLFSF5 CKLFSF6 CKLFSF7 CKLFSF8 CMKLR1 CMKOR1 CSF3 CX3CL1 CX3CL1 CX3CR1 CXCL1 CXCL10 Colorectal_cancer_KEGG 78 RAC1 K RAC2 RAC3 RAF1 RALGDS SMAD2 SMAD3 SOS1 SOS2 TCF7 TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 TP53 Common_Cytokine 108 IL21 S IL22 IL24 IL26 IL3 IL4 IL5 IL6 IL7 IL8 IL9 INHA INHBA INHBB LASS1 LEFTY2 LTA LTB NODAL PDGFA PDGFB PTN SLURP1 SPP1 TGFA TGFB1 TGFB2 TGFB3 THPO TNF TNFRSF11 Complement_and_coagulation_cascades_KEGG 65 TFPI K THBD VWF DNA_Damage_Signaling_Pathway 107 PCNA S PDCD8 PMS1 PMS2 PMS2L4 PMS2L9 PNKP PPP1R15A PRKDC RAD1 RAD17 RAD18 RAD21 RAD23A RAD23B RAD50 RAD51 RAD51C RAD51L1 RAD51L3 RAD52 RAD54L RAD9A RBBP8 REV1L RPA1 RPA3 SEMA4A SESN1 SMC1L1 SUMO1 ECM_extracellular 156 ECM1 S EFEMP1 EFEMP2 ELN EMILIN1 EMILIN2 ESAM FANK1 FBLN1 FBLN2 FBLN5 FBN1 FBN2 FBN3 FCN1 FCN2 FCN3 FLRT1 FLRT2 FLRT3 FN1 FSD1 HAPLN1 HAPLN2 HAPLN3 HAPLN4 HSPG2 IBSP IMPG1 IMPG2 LAMA1 ECM_inhibitors&other_enzymes 82 SERPING1 S SERPINH1 SERPINI1 SERPINI2 SPAM1 SPG20 SPG21 SPG3A SPG7 TGM1 TGM2 TGM3 TGM4 TGM5 TGM6 TGM7 TIMP1 TIMP2 TIMP3 TIMP4 ECM_membrane_cell-cell_adhesion 138 PCDH18 S PCDH19 PCDH20 PCDH21 PCDH7 PCDH8 PCDH9 PCDHA1 PCDHA10 PCDHA11 PCDHA12 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA6 PCDHA7 PCDHA8 PCDHA9 PCDHAC1 PCDHAC2 PCDHB1 PCDHB10 PCDHB11 PCDHB12 PCDHB13 PCDHB14 PCDHB15 PCDHB16 PCDHB17 ECM_membrane_cell-matrix_adhesion 161 PIGQ S PLXDC1 PLXDC2 PLXNA1 PLXNA2 PLXNA3 PLXNA4A PLXNA4B PLXNB1 PLXNB2 PLXNB3 PLXNC1 PLXND1 PUNC SDC2 SDC4 SEMA3A SEMA3B SEMA3C SEMA3D SEMA3E SEMA3F SEMA3G SEMA4A SEMA4B SEMA4C SEMA4D SEMA4F SEMA4G SEMA5A SEMA5B ECM_proteases 204 CPM S CPN1 CPN2 CPXM CPXM2 CTSB CTSC CTSD CTSE CTSF CTSG CTSH CTSK CTSL CTSL2 CTSLL3 CTSO CTSS CTSW CTSZ DAB1 DKFZP586 DPP10 DPP4 DPP6 DPP9 ELA1 ELA2 ELA2A ELA2B ELA3A ECM-receptor_interaction_KEGG 85 LAMC1 K LAMC2 LAMC3 LOC131873RELN SDC1 SDC2 SDC3 SDC4 SPP1 SV2A SV2B SV2C THBS1 THBS2 THBS3 THBS4 TNC TNN TNR TNXB VTN VWF EGF_PDGF_Signaling_Pathway 96 MMP7 S NFATC3 NFKB1 NRAS PDGFA PDGFB PDGFRA PDGFRB PDPK1 PIK3CA PIK3CB PIK3R1 PIK3R2 PLCG1 PLCG2 PPP2CA PRKCA PTEN PTPN11 RAF1 RAP1A RASA1 RPS6KA5 RPS6KB1 RPS6KB2 SFN SHC1 SRC STAT1 STAT3 STAT5A Endothelial_Cell_Biology 121 IL1B S IL3 IL6 IL7 IL8 ITGA5 ITGAV ITGB1 ITGB3 KDR KIT KLK3 LTB4R MAS1 MMP1 MMP14 MMP2 MMP9 NOS2A NOS3 NPPB NPR1 OCLN PDGFRA PDGFRB PECAM1 PF4 PGF PLAT PLAU PLG Focal_adhesion_KEGG 193 GRB2 K GRLF1 GSK3B HGF HRAS IBSP IGF1 IGF1R ILK ITGA10 ITGA11 ITGA2 ITGA2B ITGA3 ITGA4 ITGA5 ITGA6 ITGA7 ITGA8 ITGA9 ITGAV ITGB1 ITGB3 ITGB4 ITGB5 ITGB6 ITGB7 ITGB8 JUN KDR LAMA1 Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 MC2R S MC3R MC4R MC5R MTNR1A MTNR1B OPRD1 OPRK1 OPRL1 OPRM1 OXT P2RX4 P2RY1 P2RY11 P2RY12 P2RY2 P2RY4 P2RY6 PTGDR PTGER2 PTGER3 PTGER4 PTGFR PTHR2 RGR SSTR1 SSTR2 SSTR3 SSTR4 SSTR5 TRHR G_Protein-Coupled_Receptor_II 97 MAP3K5 S MAPK10 MKNK2 MMD NMU2R NPY1R NTN1 NTSR2 PTK2B RAI3 RAMP1 RAMP2 RAMP3 RGS10 RGS11 RGS12 RGS13 RGS16 RGS2 RGS20 RGS3 RGS4 RGS7 RGS9 SREB3 TAS2R1 TAS2R13 TAS2R14 TAS2R7 TAS2R8 TAS2R9 Gap_junction_KEGG 95 PDGFRB K PLCB1 PLCB2 PLCB3 PLCB4 PRKACA PRKACB PRKACG PRKCA PRKCB1 PRKCG PRKG1 PRKG2 PRKX PRKY RAF1 SOS1 SOS2 SRC TJP1 TUBA1 TUBA2 TUBA3 TUBA4 TUBA8 TUBB TUBB1 TUBB2B TUBB2C TUBB3 TUBB4 Genes_constituting_the_PI3_kinase_predictor 132 LMNB2 Potti et al. MAC30 MAD2L1 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MGC10993MGC13096MGC20419MGC23280MGC35521MGC4504 MGC4692 MSH2 MSH6 MTHFD1 MYB NASP NOL5A PCNA PDXP PEX5 Pfs2 POLA2 POLD1 POLD3 POLR1B Genome_Stability_DNA_Repair 113 PMS2L9 S PNKP POLD3 POLL PRKDC RAD18 RAD21 RAD23A RAD23B RAD50 RAD51 RAD51C RAD51L1 RAD51L3 RAD52 RAD54B RAD54L RFC1 RPA1 RPA3 SLK SMUG1 TDG TEP1 TERF1 TERF2 TERF2IP TERT TINF2 TNKS TNKS1BP1 G-Protein_Coupled_Receptors_Signaling 99 MMP9 S MYC NOS2A NPPA NPY OPRD1 OPRK1 PDPK1 PIK3CG POLYDOM PRIC285 PRKCA PRL PTGDR PTGER1 PTGS2 RGS2 RHO SCYA2 SCYA4 SERPINE1 SSI-1 SSI-3 TNF TSHR UCP1 VCAM1 VEGF YWHAZ ßAGTR2 ßAKT1 G-Proteins_&_Signaling_Molecules 96 PIK3CB S PLCB1 PLCB2 PLCB4 PLD1 PLD2 PLD3 PRKACA PRKACB PRKAR1A PRKAR1B PRKAR2B PRKCA PRKCB1 PRKCE PRKCG PRKCM PTK2 PTK2B PXN PYGB PYGL PYGM RAF1 RAP1A RASA1 RDX ROCK1 SHC1 SOS1 SRC Growth_Factor 84 MDK S NDP NGFB NODAL NRG1 NRG2 NRG3 NRTN NTF3 OKL38 PDGFC PGF PSPN PTN SLCO1A2 SPP1 TDGF1 TGFB1 THPO TNNT1 VEGF VEGFC Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 IL12RB1 S IL12RB2 IL13 IL13RA1 IL13RA2 IL15 IL15RA IL16 IL17 IL17C IL17R IL18 IL18R1 IL1A IL1B IL1R1 IL1R2 IL1RN IL2 IL20 IL21 IL22 IL2RA IL2RB IL2RG IL3 IL4 IL5 IL5RA IL6 IL6R Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 GRB2 S GSK3A GSK3B GYS1 GYS2 HK2 HRAS IGF1R IGF2 IGFBP1 IKBKB INPP5D INS INSL3 INSR IRS1 IRS2 IRS4 KIAA1303 KRAS LIPE MAP2K1 MAP2K2 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 MKNK1 MKNK2 NRAS Interferon 84 IL6R S IL7R IL9R IRF1 IRF2 IRF2BP1 IRF2BP2 IRF3 IRF4 IRF5 IRF6 IRF7 IRF8 IRGM LEPR MPL MX1 OAS1 PSME1 PYHIN1 SP110 TTN Interferon_a,b_Response 96 MAP2K1 S MET MNT MX1 MX2 MYC MYD88 NMI NRG1 OAS1 OAS2 OASL PLA2G1B PML PRKCZ PRKRA PRKRIP1 PSME2 PTTG1 RCBTB1 SAMSN1 SH2D1A SLC1A2 SOCS1 SOCS3 STAT1 STAT2 TAP1 TNFSF10 TNFSF7 TRIM22 Interleukins_and_Receptors 71 IL7 S IL7R IL8 IL8RA IL8RB IL9 IL9R ßFIL1 ßIL1R1 Invasiveness_Gene_Signature 189 GABARAPL Liu et al. GABARAPLHSPA2 ARPC5 CSNK2A1 PREPL ATP13A3 TUBB C1ORF121 CD59 DNAJC13 PDE8A WEE1 AIM1 DCUN1D4 SKIV2L2 C5ORF21 CEP350 CASP8 CG018 GAPDH SFPQ ERBB4 LARS NAT10 DHRS4 FAM53C NOL8 BDH2 C16ORF33 C17ORF71 JAK_STAT_Signaling_Pathway 179 IFNAR2 S IFNB1 IFNE1 IFNG IFNGR1 IFNGR2 IFNK IFNW1 IGHG3 IL10 IL10RA IL10RB IL11 IL11RA IL12A IL12B IL12RB1 IL12RB2 IL13 IL13RA1 IL13RA2 IL15 IL15RA IL19 IL2 IL20 IL20RA IL21 IL21R IL22 IL22RA1 MAP_Kinase_Signaling_Pathway 97 MAP3K7 S MAP4K1 MAP4K3 MAPK1 MAPK1) MAPK10 MAPK11 MAPK12 MAPK13 MAPK14 MAPK3 MAPK6 MAPK7 MAPK8 MAPK8IP2 MAPK9 MAPKAPK2MAPKAPK3MAX MEF2C MKNK1 MOS MST1 MYC NFATC4 NRAS PAK1 PAK3 RAC1 RAC2 RAF1 Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 SEPN1 S SEPP1 SEPW1 SFXN2 SLC11A1 SLC11A2 SLC30A1 SLC30A3 SLC30A4 SLC30A5 SLC30A6 SLC30A8 SLC31A1 SLC31A2 SLC39A1 SLC39A2 SLC39A3 SLC39A4 SLC39A6 SLC39A7 SLC40A1 SOD1 SOD2 SPS2 TF TFR2 TFRC UBE TH TLR4 TXNRD1 TXNRD2 Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 NCR3 K NFAT5 NFATC1 NFATC2 NFATC3 NFATC4 NRAS PAK1 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PLCG1 PLCG2 PPP3CA PPP3CB PPP3CC PPP3R1 PRF1 PRKCA PRKCB1 PRKCG PTK2B PTPN11 PTPN6 RAC1 RAC2 Neuroscience_Ion_Channels_&_Transporters 104 KCNN2 S KCNN3 KCNN4 KCNQ1 KCNQ2 KCNQ3 KCNQ4 KCNS1 KCNS2 KCNS3 LBP PLTP SCAMP2 SCN1A SCN1B SCN2A2 SCN2B SCN3A SCN4A SCN5A SCN7A SCN8A SCN9A SCP2 SLC15A2 SLC18A1 SLC18A2 SLC18A3 SLC1A1 SLC1A2 SLC1A3 Neurotransmitter_Receptors_and_Regulators 107 GRIN1 S GRPR HCRTR2 HRH3 HTR1B HTR2A HTR3A HTR3B ICA1 KCNMA1 KCNMB4 MAOA NMBR NMUR1 NMUR2 NPY1R NPY2R PHOX2A PPYR1 PRIMA1 RAB14 RAB3A RIMS1 SLC1A3 SLC5A7 SLC6A1 SLC6A3 SLC6A4 SLC6A5 SLC6A8 SLC6A9 NFkB_Signaling_Pathway 113 MAP3K7 S MAP3K7IP1MAP3K7IP2MAPK14 MAPK3 MAPK8 MYD88 NALP12 NFKB1 NFKB2 NFKBIA PLK2 PPM1A PPP5C RAF1 REL RELA RELB RFP2 RHOA RHOC RIPK1 RIPK2 SLC20A1 STAT1 TBK1 TICAM2 TLR1 TLR10 TLR2 TLR3 Nitric_Oxide 173 GPX5 S GPX6 GRIN2D GSS HBG1 HLA-DRA HMOX1 HPRT1 HRMT1L1 HRMT1L2 HSPA4 HSPCA HSPCB ICAM1 IGFBP1 IL10 IL1B IL2 IL4 IL6 IL8 ILK INS JUN JUNB KRT1 LAMC1 LOC493869LPO MADCAM1 MBL2 Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 IL2RA S IVL JAG1 JAG2 KRT1 KRT10 KRT14 KRT5 LFNG LMO2 LOR LRP5 MAML1 MAML2 MAML3 MAP1B MAP2K7 MAPKAPK3MECT1 MFNG MGC61598MMP7 MYCL1 NCOR2 NCSTN NEURL NFKB1 NFKB2 NOTCH1 NOTCH2 NOTCH2NL Nuclear_Receptors_and_Coregulators 114 NR2F6 S NR3C1 NR3C2 NR4A1 NR4A2 NR4A3 NR5A1 NR5A2 NR6A1 NRIP1 PCAF PGR PGRMC2 PPARA PPARBP PPARD PPARG PPARGC1APPARGC1BPRIC285 PSMC3 PSMC5 PTGER3 RARA RARB RARG RBM14 RBPSUH REBBP RIPK3 RNF14 Oxidative_phosphorylation_KEGG 115 NDUFA10 K NDUFA11 NDUFA12 NDUFA13 NDUFA2 NDUFA3 NDUFA4 NDUFA4L2NDUFA5 NDUFA6 NDUFA7 NDUFA8 NDUFA9 NDUFAB1 NDUFB1 NDUFB10 NDUFB11 NDUFB2 NDUFB3 NDUFB4 NDUFB5 NDUFB6 NDUFB7 NDUFB8 NDUFB9 NDUFC1 NDUFC2 NDUFS1 NDUFS2 NDUFS3 NDUFS4 Oxidative_Stress_and_Antioxidant_Defense 84 PRNP S PTGS1 PTGS2 PXDN PXDNL RNF7 SCARA3 SELS SEPP1 SFTPD SGK2 SIRT2 SOD1 SOD2 SOD3 SRXN1 STK25 TPO TTN TXNDC2 TXNRD1 TXNRD2 p53_Signaling_Pathway 113 MYC S MYOD1 NDRG1 NF1 NFKB1 P53AIP1 PCAF PCBP4 PHB PLAGL1 PLK1 PML PMP22 PPM1D PPP1R13B PPP1R9B PRKCA PRKCQ PTEN PTTG1 PYCARD RAI RB1 RELA RPRM SCGB3A1 SESN1 SESN2 SESN3 SFN SHC1 Passerini_Proliferation 65 IL6 msigdb PPM1D FLT3 Phosphatases 105 DUPD1 present_study EPM2A RNGTT STYX SSH1 SSH2 SSH3 PTP4A1 PTP4A2 PTP4A3 CDC14A CDC14B CDKN3 PTPDC1 PTEN TPTE2 TPTE TNS1 TENC1 MTM1 MTMR1 MTMR2 MTMR4 SBF1 MTMR6 MTMR8 MTMR9 SBF2 ACP1 CDC25A CDC25B PI3K-AKT_Signaling_Pathway 113 MAPK8 S MAPK8IP1 MKNK1 MLLT7 MTCP1 MYD88 NFKB1 NFKBIA PABPC1 PAK1 PDGFRA PDK1 PDK2 PDPK1 PIK3CA PIK3CB PIK3CG PIK3R1 PIK3R2 PIK3R3 PR48 PRKAR1B PRKCA PRKCB1 PRKCZ PTEN PTK2 PTPN11 RAC1 RAF1 RASA1 PPAR_signaling_pathway_KEGG 67 SLC27A5 K SLC27A6 SORBS1 UBC UCP1 Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 FGF21 K FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FKSG30 FN1 GIT1 GNA12 GNA13 GNG12 GRLF1 GSN HRAS INS IQGAP1 IQGAP2 IQGAP3 ITGA10 ITGA11 ITGA2 ITGA2B Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 RPS19 K RPS2 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS27L RPS28 RPS29 RPS3 RPS3A RPS4X RPS4Y1 RPS5 RPS6 RPS7 RPS8 RPS9 RPSA UBA52 Rotterdam_signature 68 OR12D2 Jansen et al. RPL23AP7 PHF11 /// RTMEM8 NEFL ACACB Shepard_cell_proliferation 232 PTCH msigdb FSCN1 ENPEP RBBP7 IRF2 CDK7 PRKCA STAT6 ARHGEF1 BUB1B EPS8 MKI67 KRT16 PRKCM CDC14A BS69 EGFR TFDP1 LRPAP1 IGFBP4 CUL5 TPX2 FTH1 IL1A LATS1 CDK3 EPHB4 CSF1 CSE1L KIF2C PRL Shepard_neg_reg_of_cell_proliferation 116 BCL2 msigdb CUL1 UMOD IGFBP6 MDM2 VHL MLLT7 BAI1 SSTR1 NF1 CDKN2A AIF1 RARRES1 ITM1 FABP3 NF2 CDKN2B CGRRF1 POU1F1 SSTR3 SST OPRM1 NDN FABP6 CUL5 TNFRSF8 PAWR IL1A CUL4A CUL2 TOB2 Signal_Transduction_in_Cancer 98 p21Cip1 S PECAM1 PGR PIG3 PPARG PTCH PTCH2 PTGS2 SLC2A1 TF TFRC TMEPAI TNF TNFAIP3 TNFRSF10 TNFRSF6 TNFSF10 TP53 TRAF1 VCAM1 VEGF WIG1 WISP1 WNT1 WNT2 WSB1 ZNF147 A2M ABCB1 ADRA1B AKT1 Signal_Transduction_Pathway_Finder 114 IRF1 S JUN JUNB KLK2 KLK3 LEF1 LEP LTA MDM2 MMP10 MMP-7 MYC NAB2 NFKB1 NFKBIA NOS2A NRIP1 ODC1 PECAM1 PGR PPARG PRKCA PRKCB1 PRKCE PTCH PTCH2 PTGS2 RBBP8 RBP1 RBP2 SELE Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 MDM2 S MIF MT2A NFKB1 NFKBIA NOS2A PCNA POR PRDX1 PRDX2 PTGS1 PTGS2 RAD23A RAD50 SERPINE1 SOD1 SOD2 TNF TNFRSF1ATNFSF10 TNFSF6 TP53 TRADD UGT1A10 UNG XRCC1 XRCC2 XRCC4 XRCC5 CAT CCL3 Stress_Response_to_Cellular_Damage 96 HSF1 S HSPA12A HSPA2 HSPA4 HSPA5 HSPA6 HSPA8 HSPA9B HSPB1 HSPB2 HSPB3 HSPCA HSPCB HSPD1 HSPE1 HSPH1 HYOU1 MAOA MAOB MGST1 NAT2 NNMT NUDT1 PON3 PPID SERPINH1 SOD1 SOD2 ST13 TCP1 TPMT T_cell_receptor_signaling_pathway_KEGG 92 PAK6 K PAK7 PDCD1 PDK1 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PLCG1 PPP3CA PPP3CB PPP3CC PPP3R1 PRKCQ PTPN6 PTPRC RASGRP1 RHOA SOS1 SOS2 TEC TNF VAV1 VAV2 VAV3 ZAP70 T-cell_and_B-cell_Activation 66 IL2RA S IL3 IL31RA IL4 TGF-beta_signaling_pathway 116 ID1 S ID2 ID3 ID4 IFNG IGF1 IGFBP3 IL6 INHBA INHBB INHBC INHBE LEFTY2 LTBP1 MAPK1 MAPK3 MYC NODAL NOG PITX2 PPP2CA PPP2CB RBL1 RBL2 RBX1 RHOA ROCK1 ROCK2 RPS6KB1 RPS6KB2 SKP1A Th1-Th2-Th3 62 S Tight_junction_KEGG 114 LOC150084 K MAGI1 MAGI2 MAGI3 MLLT4 MPDZ MPP5 MRAS MYH10 MYH14 MYH9 MYL6 NRAS OCLN PARD3 PARD6A PARD6B PARD6G PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R2A PPP2R2B PPP2R2C PPP2R3A PPP2R3B PPP2R4 PRKCA PRKCB1 PRKCD TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 NFKB1 K NFKB2 NFKBIA PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 RAC1 RELA STAT1 TBK1 TICAM1 TICAM2 TIRAP TLR1 TLR2 TLR3 TLR4 TLR5 TLR7 TLR9 TNF TOLLIP TRAF6 Toxicology_&_Drug_Resistance 73 COMT S CRABP1 CRYAA CRYAB CSF2 CTPS CXCL10 CYP11A1 CYP11B2 CYP1A1 CYP1A2 TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 TNFRSF21 S TNFRSF25 TNFRSF4 TNFRSF6BTNFRSF7 TNFSF14 TNFSF15 TNFSF7 Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 RAC3 K RAF1 SH2D2A SHC2 SPHK1 SRC VEGF vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 FZD8 S FZD9 GSK3A GSK3B JUN KREMEN1 KREMEN2 LEF1 LRP5 LRP6 MAP3K7 MAPK10 MAPK8 MAPK9 MARK4 MMP7 MYC NFAT5 NFATC1 NFATC2 NFATC3 NFATC4 NKD1 NKD2 NLK PITX2 PLCB1 PLCB2 PLCB3 PLCB4 PORCN

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 4

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K Androgen_Signaling_and_Prostate_Cancer 96 S CALR CCND1 RAB5A Angiogenesis 113 S TGFA TGFB1 TGFB2 TGFB3 TGFBR1 THBS1 THBS2 TIE TIMP1 TIMP2 TIMP3 TNF TNFAIP2 TNFRSF12 TNFSF15 TNNT1 VEGF VEGFB VEGFC VG5Q Antigen_processing_and_presentation_KEGG 73 K Apoptosis 163 S LTBR MAP3K14 MCL1 MYD88 NFKB1 NFKB2 NFKBIA NGFB NOL3 NTRK1 PDCD8 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PPP3CA PPP3CB PPP3CC PPP3R1 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B PYCARD Breast_Cancer_Estrogen_Signaling 101 msigdb BAD BCL2L2 GNAS CDKN1A COL6A1 BAG1 PTEN ACTB Calcium_signaling_pathway_KEGG 171 K MYLK MYLK2 NOS1 NOS2A NOS3 NTSR1 OXTR P2RX1 P2RX2 P2RX3 P2RX4 P2RX5 P2RX7 P2RXL1 PDE1A PDE1B PDE1C PDGFRA PDGFRB PHKA1 PHKA2 PHKB PHKG1 PHKG2 PLCB1 PLCB2 PLCB3 PLCB4 PLCD1 PLCD3 PLCD4 Cell_adhesion_molecules_(CAMs)_KEGG 125 K NCAM1 NCAM2 NEGR1 NEO1 NLGN1 NLGN2 NLGN3 NRCAM NRXN1 NRXN2 NRXN3 OCLN PDCD1 PDCD1LG2PECAM1 PTPRC PTPRF PTPRM PVR PVRL1 PVRL3 SDC1 SDC2 SDC3 SDC4 SELE SELL SELP SELPLG SIGLEC1 SPN Cell_Cycle 89 S Cell_Proliferation 72 Rosenwald et al. Chemokine_Ligand_Receptor 169 S CXCL10 CXCL11 CXCL11 CXCL12 CXCL12 CXCL13 CXCL13 CXCL14 CXCL14 CXCL15 CXCL16 CXCL16 CXCL2 CXCL2 CXCL3 CXCL3 CXCL4 CXCL5 CXCL5 CXCL6 CXCL6 CXCL7 CXCL8 CXCL9 CXCL9 CXCR1 CXCR2 CXCR3 CXCR4 CXCR5 CXCR6 Colorectal_cancer_KEGG 78 K Common_Cytokine 108 S TNFSF10 TNFSF11 TNFSF12 TNFSF13 TNFSF13B TNFSF14 TNFSF15 TNFSF18 TNFSF4 TNFSF7 TNFSF8 TNFSF9 VEGF VEGFB MDK Complement_and_coagulation_cascades_KEGG 65 K DNA_Damage_Signaling_Pathway 107 S TP53 TP73 TREX1 TREX2 UNG UNG2 XPA XPC XRCC1 XRCC2 XRCC3 XRCC4 XRCC5 ZAK ECM_extracellular 156 S LAMA2 LAMA3 LAMA4 LAMA5 LAMB1 LAMB2 LAMB3 LAMB4 LAMC1 LAMC2 LAMC3 LEPRE1 MATN1 MATN2 MATN3 MATN4 MGP NID1 NID2 NTN1 NTN2L NTN4 NTNG1 NTNG2 PAPLN PCOLCE PCOLCE2 PCOTH PRG1 PRG2 PRG3 ECM_inhibitors&other_enzymes 82 S ECM_membrane_cell-cell_adhesion 138 S PCDHB18 PCDHB19PPCDHB2 PCDHB3 PCDHB4 PCDHB5 PCDHB6 PCDHB7 PCDHB8 PCDHB9 PCDHGA1 PCDHGA10PCDHGA11PCDHGA12PCDHGA2 PCDHGA3 PCDHGA4 PCDHGA5 PCDHGA6 PCDHGA7 PCDHGA8 PCDHGA9 PCDHGB1 PCDHGB2 PCDHGB3 PCDHGB4 PCDHGB5 PCDHGB6 PCDHGB7 PCDHGB8PPCDHGC3 ECM_membrane_cell-matrix_adhesion 161 S SEMA6A SEMA6B SEMA6C SEMA6D SEMA7A SGCA SGCB SGCD SGCE SGCG SGCZ SLITRK1 SLITRK2 SLITRK3 SLITRK4 SLITRK5 SLITRK6 TSPAN1 TSPAN10 TSPAN12 TSPAN13 TSPAN14 TSPAN15 TSPAN16 TSPAN17 TSPAN18 TSPAN2 TSPAN3 TSPAN31 TSPAN32 TSPAN33 ECM_proteases 204 S ELA3B ENPEP FLJ25084 GZMA GZMB GZMH GZMK GZMM HPN HTRA1 HTRA3 IMMP1L IMMP2L IMP5 ITIH4 KEL KLK1 KLK10 KLK11 KLK12 KLK13 KLK14 KLK15 KLK2 KLK3 KLK4 KLK5 KLK6 KLK7 KLK8 KLK9 ECM-receptor_interaction_KEGG 85 K EGF_PDGF_Signaling_Pathway 96 S SYP TNFSF6 TP53 Endothelial_Cell_Biology 121 S PTGIS PTGS2 RHOB RIPK1 SELE SELL SELPLG SERPINE1 SOD1 SPHK1 TEK TFPI TFPI2 THBD THBS1 TIMP1 TNF TNFAIP3 TNFRSF10 TNFRSF10 TNFRSF11 TNFRSF6 TNFSF10 TNFSF6 VCAM1 VEGF VWF XDH Focal_adhesion_KEGG 193 K LAMA2 LAMA3 LAMA4 LAMA5 LAMB1 LAMB2 LAMB3 LAMB4 LAMC1 LAMC2 LAMC3 LOC131873MAP2K1 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 MET MLCK MYL6 MYLK MYLK2 PAK1 PAK2 PAK3 PAK4 PAK6 PAK7 PARVA PARVB Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 S TSHR VIPR1 VIPR2 G_Protein-Coupled_Receptor_II 97 S TM7SF1 TRAF6 UTS2 XCR1 Gap_junction_KEGG 95 K TUBB6 TUBB8 Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. POLR1C PPAT PRIM1 PRKRIR PRPS1 RAD51 RAMP RBM15 RFC2 RFC3 RHOB RNASEH2ARP13-15M1RPA3 RPP25 RRM2 SHMT1 SLBP SLC19A1 SLC25A15 SLC25A19 SPEN SSX2IP SUPT16H TAF5 TBRG4 TCF19 TLE3 TMEM18 TOP3A UBE2T Genome_Stability_DNA_Repair 113 S TNKS2 TOP3A TOP3B TP73 TREX1 UBE2A UBE2B UBE2I UBE2N UBE2V2 UNG UNG2 XAB2 XPA XPC XRCC1 XRCC2 XRCC3 XRCC4 XRCC5 G-Protein_Coupled_Receptors_Signaling 99 S ßCCND1 ßCDKN1B ßGT ADRB1 APM1 CDKN1A G-Proteins_&_Signaling_Molecules 96 S SRF STAT3 VAV1 Growth_Factor 84 S Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 S PCK1 PCK2 PDE3A PDE3B PDPK1 PFKL PFKM PFKP PHKA1 PHKA2 PHKB PHKG1 PHKG2 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PKLR PKM2 PPARGC1APPP1CA PPP1CB PPP1CC PPP1R3A PPP1R3B PPP1R3C PPP1R3D Interferon 84 S Interferon_a,b_Response 96 S TRIM34 TYK2 VEGF Interleukins_and_Receptors 71 S Invasiveness_Gene_Signature 189 Liu et al. ECHDC2 IER5 NUP37 SCNM1 CNIH4 C8ORF52 ETAA16 GTPBP1 VTCN1 NUAK2 C11ORF17 DUSP10 CHPT1 39515 DNAPTP6 TOB2 SNX6 NUCKS1 XPR1 GTF3C3 DNMT3A ZDHHC2 C1ORF163 NUDT5 MGC4399 SERTAD1 ANKRD13CC7ORF36 RAB23 LMBR1 KIAA1287 JAK_STAT_Signaling_Pathway 179 S IL22RA2 IL23A IL23R IL24 IL26 IL28A IL28B IL28RA IL29 IL2RA IL2RB IL2RG IL3 IL31RA IL3RA IL4 IL4R IL5 IL5RA IL6 IL6R IL6ST IL7 IL7R IL9 IL9R INDO INSR IRF1 ISGF3G JAK1 MAP_Kinase_Signaling_Pathway 97 S RB1 RPS6KA5 SFN TP53 Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 S VEGF Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K RAC3 RAF1 SH2D1B SH3BP2 SHC1 SHC2 SHC3 SHC4 SOS1 SOS2 SYK TNF TNFRSF10 TNFRSF10 TNFRSF10 TNFRSF10 TNFSF10 TYROBP ULBP1 ULBP2 ULBP3 VAV1 VAV2 VAV3 ZAP70 Neuroscience_Ion_Channels_&_Transporters 104 S SLC25A3 SLC25A4 SLC25A5 SLC29A1 SLC2A1 SLC2A11 SLC33A1 SLC35B1 SLC6A11 SLC6A12 SLC6A2 Neurotransmitter_Receptors_and_Regulators 107 S SNAP25 SNAPAP SNPH SORCS1 SORCS2 SSTR1 SSTR2 SSTR3 SSTR4 SYN1 SYN2 SYN3 SYT1 TACR1 NFkB_Signaling_Pathway 113 S TLR4 TLR6 TLR7 TLR8 TLR9 TNF TNFAIP3 TNFRSF10 TNFRSF10 TNFRSF1ATNFRSF5 TNFRSF7 TNFSF10 TNFSF14 TNFSF6 TRADD TRAF5 TRAF6 TRIF VAPA Nitric_Oxide 173 S MMP1 MMP2 MMP7 MMP9 MPO MRP1-EST MSRA MT1G MT3 MTL5 MYB MYC NCAM1 NCF1 NCF2 NFKBIA NME5 NOS1 NOS2A NOS3 NOX5 NQO1 NUDT1 OGG1 OPRM1 OXR1 PDGFA PDGFB PLA2G2D PLAT PNKP Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S NOTCH3 NOTCH4 NR4A2 NUMB NUMBL PAX5 PCAF PDPK1 PEN2 POFUT1 PPARG PSEN1 PSEN2 PSENEN PTCH PTCRA RBPSUH RBPSUHL RFNG RUNX1 SEL1L SH2D1A SHH SIL SKIIP SMO SNW1 SPEN STAT6 SUFU SUPT6H Nuclear_Receptors_and_Coregulators 114 S RORA RORB RORC RXRA RXRB RXRG SIX3 SKIIP SRCAP TGFB1I1 THRA THRAP1 THRAP3 THRAP4 THRAP5 THRAP6 THRB TIF1 TRERF1 TRIP4 VDR Oxidative_phosphorylation_KEGG 115 K NDUFS5 NDUFS6 NDUFS7 NDUFS8 NDUFV1 NDUFV2 NDUFV3 PPA1 PPA2 SDHA SDHB SDHC SDHD TCIRG1 UCRC UQCR UQCRB UQCRC1 UQCRC2 UQCRFS1 UQCRH UQCRQ Oxidative_Stress_and_Antioxidant_Defense 84 S p53_Signaling_Pathway 113 S SIAH1 SIRT1 SMARCB1 SNCA STAT1 TADA3L TNF TNFRSF10 TNFSF6 TP53 TP53BP2 TP73 TP73L TRAF2 TRAF4 TRAF5 TSC1 TSC2 TSHR WT1 Passerini_Proliferation 65 msigdb Phosphatases 105 present_study CDC25C EYA1 EYA2 EYA3 EYA4 MTMR10 MTMR11 MTMR12 KIAA1018 MTMR3 MTMR7 MTMR15 PI3K-AKT_Signaling_Pathway 113 S RBL2 RHEB RHOA RPS6 RPS6KA1 RPS6KB1 SHC1 SOS1 SRF TCL1A TCL1B TIRAP TLR4 TOLLIP TSC1 TSC2 WASL WNT1 YWHAH ZFYVE21 PPAR_signaling_pathway_KEGG 67 K Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K ITGA3 ITGA4 ITGA5 ITGA6 ITGA7 ITGA8 ITGA9 ITGAE ITGAL ITGAM ITGAV ITGAX ITGB1 ITGB2 ITGB3 ITGB4 ITGB5 ITGB6 ITGB7 ITGB8 KRAS LIMK2 MAP2K1 MAP2K2 MAPK1 MAPK3 MATK MLCK MOS MRAS MSN Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K Rotterdam_signature 68 Jansen et al. Shepard_cell_proliferation 232 msigdb SERPINF1 PDZK1 PRG4 CDC2L2 PCNA IL3 FES TNFRSF9 AKR1C3 SFN CDK4 KNSL7 THPO UNQ429 CDK5 IL13 C8FW HDGF PRDX1 GFI1B BLZF1 DUSP22 IL5RA CD81 MT3 CDC16 MYC ERBB4 MAS1 NAB2 TM4SF1 Shepard_neg_reg_of_cell_proliferation 116 msigdb COL4A3 C16orf3 CD164 GAS1 PRKRA CXCL1 PRKRIR RBBP4 PLG CDKN2C DRIM GPNMB SIRPB2 KLF4 CDC7 TNFRSF9 ING1 SESN1 MDM4 ADAMTS1 CDKN1A NCK2 PCAF Signal_Transduction_in_Cancer 98 S BAX BMP2 CDK2 HSF1 ICAM1 Signal_Transduction_Pathway_Finder 114 S SELPLG TANK TCF7 TERT TFRC TMEPA1 TNF TNFRSF10 TNFRSF6 TNFSF6 TP53 TP53I3 TRIM25 VCAM1 VEGF WISP1 WISP2 WISP3 WNT1 WNT2 WSB1 Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 S CCNC CDKN1A DNAJA1 Stress_Response_to_Cellular_Damage 96 S TRA1 UGT1A10 XDH T_cell_receptor_signaling_pathway_KEGG 92 K T-cell_and_B-cell_Activation 66 S TGF-beta_signaling_pathway 116 S SMAD1 SMAD2 SMAD3 SMAD5 SMAD6 SMAD7 SMAD9 SMURF1 SMURF2 SP1 TFDP1 TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 THBS1 THBS2 THBS3 THBS4 TNF ZFYVE16 ZFYVE9 Th1-Th2-Th3 62 S Tight_junction_KEGG 114 K PRKCE PRKCG PRKCH PRKCI PRKCQ PRKCZ PTEN RAB13 RAB3B RHOA RRAS RRAS2 SPTAN1 SRC SYMPK TJAP1 TJP1 TJP2 VAPA YES1 ZAK TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K Toxicology_&_Drug_Resistance 73 S TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 S Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 K vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 S PPARD PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R2A PPP2R2B PPP2R2C PPP3CA PPP3CB PPP3CC PPP3R1 PRICKLE1 PRICKLE2 PRKACA PRKACB PRKACG PRKCA PRKCB1 PRKCG PRKX PRKY PSEN1 PYGO1 PYGO2 RAC1 RAC2 RAC3 RBX1 RHOA RHOU

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 5

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K Androgen_Signaling_and_Prostate_Cancer 96 S Angiogenesis 113 S Antigen_processing_and_presentation_KEGG 73 K Apoptosis 163 S RELA RIPK1 RIPK2 TNF TNFRSF10 TNFRSF10 TNFRSF10 TNFRSF10 TNFRSF11 TNFRSF12 TNFRSF14 TNFRSF19 TNFRSF1ATNFRSF1BTNFRSF21 TNFRSF25 TNFRSF5 TNFRSF6 TNFRSF6BTNFRSF7 TNFRSF9 TNFSF10 TNFSF14 TNFSF18 TNFSF5 TNFSF6 TNFSF7 TNFSF8 TNFSF9 TP53 TP53BP2 Breast_Cancer_Estrogen_Signaling 101 msigdb Calcium_signaling_pathway_KEGG 171 K PLCE1 PLCG1 PLCG2 PLCZ1 PLN PPID PPP3CA PPP3CB PPP3CC PPP3R1 PRKACA PRKACB PRKACG PRKCA PRKCB1 PRKCG PRKX PRKY PTAFR PTGER1 PTGER3 PTGFR PTK2B RP11-145HRYR1 RYR2 RYR3 SLC25A4 SLC25A5 SLC25A6 SLC8A1 Cell_adhesion_molecules_(CAMs)_KEGG 125 K VCAM1 Cell_Cycle 89 S Cell_Proliferation 72 Rosenwald et al. Chemokine_Ligand_Receptor 169 S CYFIP2 ECGF1 EPO FY GDF5 GPR109B GPR2 GPR31 GPR77 GPR81 HIF1A IL13 IL16 IL18 IL1A IL4 IL8 IL8RA IL8RB LTB4R MMP2 MMP7 MYD88 NFKB1 PF4 PPBP PRL RGS13 RGS3 SCYE1 SDF2 Colorectal_cancer_KEGG 78 K Common_Cytokine 108 S Complement_and_coagulation_cascades_KEGG 65 K DNA_Damage_Signaling_Pathway 107 S ECM_extracellular 156 S PRG4 SDF2 SLIT1 SLIT2 SLIT3 SMC3 SMOC2 SNED1 SPARC SPARCL1 SPOCK1 SPOCK2 SPOCK3 SPON1 SPON2 STAG1 STAG3 STIM1 STIM2 THBS1 THBS2 THBS3 THBS4 THSD3 THSD4 TNC TNN TNR TNXA TNXB VTN ECM_inhibitors&other_enzymes 82 S ECM_membrane_cell-cell_adhesion 138 S PCDHGC4 PCDHGC5 PCLKC PECAM1 ROBO1 ROBO2 ROBO3 ROBO4 SELE SELL SELP SELPLG TCAM1 VCAM1 ECM_membrane_cell-matrix_adhesion 161 S TSPAN4 TSPAN5 TSPAN6 TSPAN7 TSPAN8 TSPAN9 ASAM BST1 BST2 CNTN1 CNTN2 CNTN3 CNTN4 CNTN5 CNTN6 CNTNAP1 CNTNAP2 CNTNAP3 CNTNAP3BCNTNAP4 CNTNAP5 SIGLEC1 SIGLEC10 SIGLEC11 SIGLEC5 SIGLEC6 SIGLEC7 SIGLEC8 SIGLEC9 SIGLECP16SIGLECP3 ECM_proteases 204 S KLKB1 Klkbl4 LMLN LONRF2 LONRF3 MASP1 MASP2 MBTPS2 MME MMEL1 MMP1 MMP10 MMP11 MMP12 MMP13 MMP14 MMP15 MMP16 MMP17 MMP19 MMP2 MMP20 MMP21 MMP23A MMP23B MMP24 MMP25 MMP26 MMP27 MMP28 MMP3 ECM-receptor_interaction_KEGG 85 K EGF_PDGF_Signaling_Pathway 96 S Endothelial_Cell_Biology 121 S Focal_adhesion_KEGG 193 K PARVG PDGFB PDGFC PDGFD PDGFRA PDGFRB PDPK1 PGF PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PIP5K1C PPP1CA PPP1CB PPP1CC PPP1R12A PRKCA PRKCB1 PRKCG PTEN PTK2 PXN RAC1 RAC2 RAC3 RAF1 Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 S G_Protein-Coupled_Receptor_II 97 S Gap_junction_KEGG 95 K Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. UHRF1 UMPS UNG ZMYND19 ZNF367 ZNF45 ZNF473 ZWINT Genome_Stability_DNA_Repair 113 S G-Protein_Coupled_Receptors_Signaling 99 S G-Proteins_&_Signaling_Molecules 96 S Growth_Factor 84 S Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 S PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKACA PRKACB PRKACG PRKAG1 PRKAG3 PRKAR1A PRKAR1B PRKAR2A PRKAR2B PRKCI PRKCZ PRKX PRKY PTPN1 PTPRF PYGB PYGL PYGM RAF1 RAPGEF1 RHEB RHOQ RPS6 RPS6KB1 RPS6KB2 SH2B2 SHC1 Interferon 84 S Interferon_a,b_Response 96 S Interleukins_and_Receptors 71 S Invasiveness_Gene_Signature 189 Liu et al. ETNK1 C10ORF9 WDR68 ABHD14B TMEM101 GOPC AGPS SLC25A25 METTL2B METTL2A PILRB MTERFD3 ZYG11B CCDC43 ALG2 THUMPD3 UBE2F C6ORF107 KIAA1600 GSK3B SCYL1BP1 TMC4 C1ORF80 ELL2 C21ORF86 LOC255783MGC45840SGK3 SORBS2 FLJ39370 TICAM2 JAK_STAT_Signaling_Pathway 179 S JAK2 JAK3 JUN JUNB LEP LEPR LIF LIFR MAF MPL MYC OSM OSMR PIAS1 PIAS2 PIAS3 PIAS4 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PIM1 PRL PRLR PTPN11 PTPN6 SOCS1 MAP_Kinase_Signaling_Pathway 97 S Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 S Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K Neuroscience_Ion_Channels_&_Transporters 104 S Neurotransmitter_Receptors_and_Regulators 107 S NFkB_Signaling_Pathway 113 S Nitric_Oxide 173 S POLYDOM PPP1R15A PPP3CA PRDX2 PRDX5 PRDX6 PREX1 PRG3 PRKAR1B PRKCA PRKDC PRKG1 PRMT3 PRNP PTGS2 RNF7 S100A10 SCARA3 SCRT2 SELS SEPP1 SERPINE1 SFTPA1 SGK2 SHC1 SIRT2 SLC6A6 SLC7A1 SLC7A2 SOD1 SOD2 Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S TEAD1 TLE1 TLE1 ADAMWISP1 WNT11 ZIC2 Nuclear_Receptors_and_Coregulators 114 S Oxidative_phosphorylation_KEGG 115 K Oxidative_Stress_and_Antioxidant_Defense 84 S p53_Signaling_Pathway 113 S Passerini_Proliferation 65 msigdb Phosphatases 105 present_study PI3K-AKT_Signaling_Pathway 113 S PPAR_signaling_pathway_KEGG 67 K Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K MYH10 MYH14 MYH9 MYL1 MYL3 MYLK MYLK2 NCKAP1 NCKAP1L NRAS PAK1 PAK2 PAK3 PAK4 PAK6 PAK7 PDGFB PDGFRA PDGFRB PFN1 PFN2 PFN3 PFN4 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K Rotterdam_signature 68 Jansen et al. Shepard_cell_proliferation 232 msigdb NUDC IL1B FGF5 LGI1 TIEG APRIN HDGFRP3 EDNRA IL6R LAMA1 CD160 LRP1 FZD3 GRPR IL8RB BCAR1 GAB1 TSPY ERBB2 ZFP36L2 RFP OSM AREG BCAT1 GSPT1 RAF1 PEMT MAD1L1 MNAT1 MAD S100A6 Shepard_neg_reg_of_cell_proliferation 116 msigdb Signal_Transduction_in_Cancer 98 S Signal_Transduction_Pathway_Finder 114 S Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 S Stress_Response_to_Cellular_Damage 96 S T_cell_receptor_signaling_pathway_KEGG 92 K T-cell_and_B-cell_Activation 66 S TGF-beta_signaling_pathway 116 S Th1-Th2-Th3 62 S Tight_junction_KEGG 114 K TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K Toxicology_&_Drug_Resistance 73 S TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 S Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 K vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 S ROCK1 ROCK2 RUVBL1 SENP2 SFRP1 SFRP2 SFRP4 SFRP5 SHFM3 SIAH1 SKP1A SLC9A3R1 SMAD2 SMAD3 SOX17 T TBL1X TBL1XR1 TBL1Y TCF7 TCF7L1 TCF7L2 TLE1 TLE2 TLE3 TLE4 TP53 VANGL1 VANGL2 WIF1 WISP1

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 6

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K Androgen_Signaling_and_Prostate_Cancer 96 S Angiogenesis 113 S Antigen_processing_and_presentation_KEGG 73 K Apoptosis 163 S TP73 TP73L TRADD TRAF1 TRAF2 TRAF3 TRAF4 TRAF5 Breast_Cancer_Estrogen_Signaling 101 msigdb Calcium_signaling_pathway_KEGG 171 K SLC8A2 SLC8A3 SPHK1 Symbol TACR1 TACR2 TACR3 TBXA2R TNNC1 TNNC2 TRHR TRPC1 TTN VDAC1 VDAC2 VDAC3 Cell_adhesion_molecules_(CAMs)_KEGG 125 K Cell_Cycle 89 S Cell_Proliferation 72 Rosenwald et al. Chemokine_Ligand_Receptor 169 S SLIT2 TCP10 TLR2 TLR4 TNF TNFRSF1ATNFSF14 TREM1 TREM2 VHL XCL1 XCL1 XCL2 XCR1 Colorectal_cancer_KEGG 78 K Common_Cytokine 108 S Complement_and_coagulation_cascades_KEGG 65 K DNA_Damage_Signaling_Pathway 107 S ECM_extracellular 156 S VWF ECM_inhibitors&other_enzymes 82 S ECM_membrane_cell-cell_adhesion 138 S ECM_membrane_cell-matrix_adhesion 161 S GPC1 GPC2 GPC3 GPC4 GPC5 GPC6 ECM_proteases 204 S MMP7 MMP8 MMP9 MMPL1 NAALAD2 NAALADL1NAPSB OMA1 OSGEP OSGEPL1 P11 PCOLN3 PGCP PHEX PREP PREPL PRSS1 PRSS12 PRSS15 PRSS16 PRSS2 PRSS21 PRSS22 PRSS23 PRSS27 PRSS3 PRSS33 PRSS35 PRSS36 PRSS7 PRSS8 ECM-receptor_interaction_KEGG 85 K EGF_PDGF_Signaling_Pathway 96 S Endothelial_Cell_Biology 121 S Focal_adhesion_KEGG 193 K RAP1A RAP1B RAPGEF1 RELN RHOA ROCK1 ROCK2 RP11-145HSHC1 SHC2 SHC3 SHC4 SOS1 SOS2 SPP1 SRC THBS1 THBS2 THBS3 THBS4 TLN1 TLN2 TNC TNN TNR TNXB TTN VASP VAV1 VAV2 VAV3 Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 S G_Protein-Coupled_Receptor_II 97 S Gap_junction_KEGG 95 K Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. Genome_Stability_DNA_Repair 113 S G-Protein_Coupled_Receptors_Signaling 99 S G-Proteins_&_Signaling_Molecules 96 S Growth_Factor 84 S Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 S SHC2 SHC3 SHC4 SKIP SLC2A4 SOCS1 SOCS2 SOCS3 SOCS6 SORBS1 SOS1 SOS2 SREBF1 TRIP10 TSC1 TSC2 Interferon 84 S Interferon_a,b_Response 96 S Interleukins_and_Receptors 71 S Invasiveness_Gene_Signature 189 Liu et al. KIAA0146 LOC130576CYP4V2 SLC44A1 APLP2 EPHX1 TMEM63A CITED4 HNMT LOC439994C4ORF7 IRX3 NGFRAP1LLOC283481THAP2 LRP2 KIAA1217 PNKD DBR1 LOC144233FLJ37953 FLJ90709 ERN1 C9ORF64 TPD52 ALKBH1 LOC388279ETS1 NEBL LRPAP1 CSTF1 JAK_STAT_Signaling_Pathway 179 S SOCS2 SOCS3 SOCS4 SOCS5 SOCS6 SOS1 SOS2 SPRED1 SPRED2 SPRY1 SPRY2 SPRY3 SPRY4 STAM STAM2 STAT1 STAT2 STAT3 STAT4 STAT5A STAT5B STAT6 TPO TSLP MAP_Kinase_Signaling_Pathway 97 S Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 S Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K Neuroscience_Ion_Channels_&_Transporters 104 S Neurotransmitter_Receptors_and_Regulators 107 S NFkB_Signaling_Pathway 113 S Nitric_Oxide 173 S SOD3 SPARC SRXN1 TFRC TGFB1 TIMP1 TNF TNFRSF1ATNFRSF6 TPO TROAP TTN TXNRD1 TXNRD2 TYR VCAM1 VEGF ZNF2 Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S Nuclear_Receptors_and_Coregulators 114 S Oxidative_phosphorylation_KEGG 115 K Oxidative_Stress_and_Antioxidant_Defense 84 S p53_Signaling_Pathway 113 S Passerini_Proliferation 65 msigdb Phosphatases 105 present_study PI3K-AKT_Signaling_Pathway 113 S PPAR_signaling_pathway_KEGG 67 K Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K PIP5K1A PIP5K1B PIP5K1C PIP5K2A PIP5K2B PIP5K2C PIP5K3 PPP1CA PPP1CB PPP1CC PPP1R12A PPP1R12B PTK2 PXN RAC1 RAC2 RAC3 RAF1 RDX RHOA ROCK1 ROCK2 RP11-145HRRAS RRAS2 SLC9A1 SOS1 SOS2 SSH1 SSH2 SSH3 Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K Rotterdam_signature 68 Jansen et al. Shepard_cell_proliferation 232 msigdb CDK5R1 TNFRSF17 APPL SLC29A2 IL11 GCG EHF PTHLH MATK IL6 CD28 PRDM4 EPAC TCFL5 PDGFRA HGF IL4 PSPHL EMP2 ZNF259 SIL CLK1 TPD52L2 NDP IL2RA BIN1 DKC1 CREG REG1B IL12B KITLG Shepard_neg_reg_of_cell_proliferation 116 msigdb Signal_Transduction_in_Cancer 98 S Signal_Transduction_Pathway_Finder 114 S Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 S Stress_Response_to_Cellular_Damage 96 S T_cell_receptor_signaling_pathway_KEGG 92 K T-cell_and_B-cell_Activation 66 S TGF-beta_signaling_pathway 116 S Th1-Th2-Th3 62 S Tight_junction_KEGG 114 K TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K Toxicology_&_Drug_Resistance 73 S TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 S Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 K vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 S WISP2 WNT1 WNT10A WNT10B WNT11 WNT16 WNT2 WNT2B WNT3 WNT3A WNT4 WNT5A WNT5B WNT6 WNT7A WNT7B WNT8A WNT8B WNT9A WNT9B

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 7

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K Androgen_Signaling_and_Prostate_Cancer 96 S Angiogenesis 113 S Antigen_processing_and_presentation_KEGG 73 K Apoptosis 163 S Breast_Cancer_Estrogen_Signaling 101 msigdb Calcium_signaling_pathway_KEGG 171 K Cell_adhesion_molecules_(CAMs)_KEGG 125 K Cell_Cycle 89 S Cell_Proliferation 72 Rosenwald et al. Chemokine_Ligand_Receptor 169 S Colorectal_cancer_KEGG 78 K Common_Cytokine 108 S Complement_and_coagulation_cascades_KEGG 65 K DNA_Damage_Signaling_Pathway 107 S ECM_extracellular 156 S ECM_inhibitors&other_enzymes 82 S ECM_membrane_cell-cell_adhesion 138 S ECM_membrane_cell-matrix_adhesion 161 S ECM_proteases 204 S PSMC4 RNPEP SPPL2A SPPL2B TMPRSS11TMPRSS11TMPRSS11TMPRSS12TMPRSS13TMPRSS2 TMPRSS3 TMPRSS4 TMPRSS5 TMPRSS6 TSP50 UNQ1887 UNQ9391 XPNPEP2 ECM-receptor_interaction_KEGG 85 K EGF_PDGF_Signaling_Pathway 96 S Endothelial_Cell_Biology 121 S Focal_adhesion_KEGG 193 K VCL VEGF VEGFB VEGFC VTN VWF ZYX Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 S G_Protein-Coupled_Receptor_II 97 S Gap_junction_KEGG 95 K Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. Genome_Stability_DNA_Repair 113 S G-Protein_Coupled_Receptors_Signaling 99 S G-Proteins_&_Signaling_Molecules 96 S Growth_Factor 84 S Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 S Interferon 84 S Interferon_a,b_Response 96 S Interleukins_and_Receptors 71 S Invasiveness_Gene_Signature 189 Liu et al. MAFF MAST4 C7ORF25 JAK_STAT_Signaling_Pathway 179 S MAP_Kinase_Signaling_Pathway 97 S Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 S Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K Neuroscience_Ion_Channels_&_Transporters 104 S Neurotransmitter_Receptors_and_Regulators 107 S NFkB_Signaling_Pathway 113 S Nitric_Oxide 173 S Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S Nuclear_Receptors_and_Coregulators 114 S Oxidative_phosphorylation_KEGG 115 K Oxidative_Stress_and_Antioxidant_Defense 84 S p53_Signaling_Pathway 113 S Passerini_Proliferation 65 msigdb Phosphatases 105 present_study PI3K-AKT_Signaling_Pathway 113 S PPAR_signaling_pathway_KEGG 67 K Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K TIAM1 TIAM2 TMSB4X TMSB4Y TMSL3 TTN VAV1 VAV2 VAV3 VCL VIL2 WAS WASF1 WASF2 WASL Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K Rotterdam_signature 68 Jansen et al. Shepard_cell_proliferation 232 msigdb TM4SF8 GRN TGFBI NR6A1 TNFSF13B EPS15 TAL1 MYT2 MTCP1 PLEKHC1 LAMP3 S100B TNFSF8 IL15 PDGFA LMO1 CDC25C NPY TNFSF9 MAPRE1 LY86 SKP2 MIA UBE2V2 CXCL1 TM4SF9 TNFSF7 MPL INSIG1 E2F1 CCKBR Shepard_neg_reg_of_cell_proliferation 116 msigdb Signal_Transduction_in_Cancer 98 S Signal_Transduction_Pathway_Finder 114 S Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 S Stress_Response_to_Cellular_Damage 96 S T_cell_receptor_signaling_pathway_KEGG 92 K T-cell_and_B-cell_Activation 66 S TGF-beta_signaling_pathway 116 S Th1-Th2-Th3 62 S Tight_junction_KEGG 114 K TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K Toxicology_&_Drug_Resistance 73 S TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 S Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 K vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 S

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Page 8

GENE SETS N. Genes Source Gene Sympbol Adherens_junction__KEGG 75 K Androgen_Signaling_and_Prostate_Cancer 96 S Angiogenesis 113 S Antigen_processing_and_presentation_KEGG 73 K Apoptosis 163 S Breast_Cancer_Estrogen_Signaling 101 msigdb Calcium_signaling_pathway_KEGG 171 K Cell_adhesion_molecules_(CAMs)_KEGG 125 K Cell_Cycle 89 S Cell_Proliferation 72 Rosenwald et al. Chemokine_Ligand_Receptor 169 S Colorectal_cancer_KEGG 78 K Common_Cytokine 108 S Complement_and_coagulation_cascades_KEGG 65 K DNA_Damage_Signaling_Pathway 107 S ECM_extracellular 156 S ECM_inhibitors&other_enzymes 82 S ECM_membrane_cell-cell_adhesion 138 S ECM_membrane_cell-matrix_adhesion 161 S ECM_proteases 204 S ECM-receptor_interaction_KEGG 85 K EGF_PDGF_Signaling_Pathway 96 S Endothelial_Cell_Biology 121 S Focal_adhesion_KEGG 193 K Folate_biosynthesis_KEGG 37 K G_Protein-Coupled_Receptor 96 S G_Protein-Coupled_Receptor_II 97 S Gap_junction_KEGG 95 K Genes_constituting_the_PI3_kinase_predictor 132 Potti et al. Genome_Stability_DNA_Repair 113 S G-Protein_Coupled_Receptors_Signaling 99 S G-Proteins_&_Signaling_Molecules 96 S Growth_Factor 84 S Hedgehog_signaling_pathway_KEGG 55 K Hypoxia_Signaling_Pathway 48 S IL18_pathway 6 msigdb IL3_Pathway 15 msigdb IL6PATHWAY 23 msigdb IL7PATHWAY 18 msigdb Inflammatory_Cytokines_&_Receptors 93 S Inositol_phosphate_metabolism_KEGG 51 K Insulin_Signaling_Pathway 171 S Interferon 84 S Interferon_a,b_Response 96 S Interleukins_and_Receptors 71 S Invasiveness_Gene_Signature 189 Liu et al. JAK_STAT_Signaling_Pathway 179 S MAP_Kinase_Signaling_Pathway 97 S Metabolism_of_xenobiotics_by_cytochrome_P450_KEGG 59 K Metal_Transport_and_Homeostasis 94 S Metalloproteases 34 present_study Metastasis_adenocarc_dn 34 msigdb Metastasis_adenocarc_up 14 msigdb mTOR_signaling_pathway_KEGG 49 K Natural_killer_cell_mediated_cytotoxicity_KEGG 118 K Neuroscience_Ion_Channels_&_Transporters 104 S Neurotransmitter_Receptors_and_Regulators 107 S NFkB_Signaling_Pathway 113 S Nitric_Oxide 173 S Nitrogen_metabolism_KEGG 24 K Notch_Signaling_Pathway 130 S Nuclear_Receptors_and_Coregulators 114 S Oxidative_phosphorylation_KEGG 115 K Oxidative_Stress_and_Antioxidant_Defense 84 S p53_Signaling_Pathway 113 S Passerini_Proliferation 65 msigdb Phosphatases 105 present_study PI3K-AKT_Signaling_Pathway 113 S PPAR_signaling_pathway_KEGG 67 K Proliferation_Signature 51 Whitfield et al. Proteasome_KEGG 31 K Recurrence_Score 16 Regulation_of_actin_cytoskeleton_KEGG 201 K Regulation_of_autophagy_KEGG 28 K Riboflavin_metabolism_KEGG 16 K Ribosome_KEGG 86 K Rotterdam_signature 68 Jansen et al. Shepard_cell_proliferation 232 msigdb IL15RA MAPRE2 IL12A DAB2 TSPAN-2 PAP CBFA2T3 TSPAN-1 CXorf15 PLK E4F1 CSF1R DCTN2 FGF6 PTEN Shepard_neg_reg_of_cell_proliferation 116 msigdb Signal_Transduction_in_Cancer 98 S Signal_Transduction_Pathway_Finder 114 S Sphingolipid_metabolism_KEGG 37 K Stress_&_Toxicity_Pathway_Finder 96 S Stress_Response_to_Cellular_Damage 96 S T_cell_receptor_signaling_pathway_KEGG 92 K T-cell_and_B-cell_Activation 66 S TGF-beta_signaling_pathway 116 S Th1-Th2-Th3 62 S Tight_junction_KEGG 114 K TNF_L&R 28 S Toll-like_receptor_signaling_pathway_KEGG 90 K Toxicology_&_Drug_Resistance 73 S TSP1_pathway 7 S Tumor_Metastasis 59 S Tumor_Necrosis_Factor 70 S Tumor_Suppressor 26 msigdb Tyrosine_metabolism_KEGG 55 K Underhill_proliferation 19 Underhill et al. VEGF_signaling_pathway_KEGG 69 K vV_70gene_Signature 61 van't Veer et al. Wnt_Signaling_Pathway 175 S

NOTE: Number of genes present in each genesets and source are indicated (msigdb= Molecular Signatures Database http://www.broad.mit.edu/gsea/msigdb/index.jsp, K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Supplemental Table 2a. Pearson correlation analysis of each MMP and COX-2 with OPN expression profiles. Dataset* I II III IV VVIVII ID GeneSymbol r P r P r P r P r P r P r P 4312 MMP1 0.01 0.983 0.04 0.818 0.05 0.815 0.43 0.070 0.13 0.235 -0.23 0.101 4313 MMP2 -0.15 0.264 -0.38 0.036 0.01 0.966 -0.42 0.067 0.13 0.231 -0.15 0.282 4314 MMP3 0.06 0.714 -0.31 0.271 -0.33 0.072 0.15 0.537 -0.17 0.479 0.02 0.875 -0.20 0.095 4316 MMP7 0.14 0.255 0.19 0.514 0.35 0.054 0.15 0.531 -0.20 0.410 0.34 0.001 0.27 0.052 4317 MMP8 -0.13 0.500 -0.08 0.730 0.05 0.854 -0.01 0.901 -0.25 0.069 4318 MMP9 0.37 0.015 0.50 0.037 0.18 0.337 0.15 0.508 0.76 0.000 0.32 0.002 0.47 0.000 4319 MMP10 -0.32 0.374 0.21 0.277 0.36 0.116 0.23 0.368 0.36 0.001 -0.34 0.012 4320 MMP11 0.12 0.483 0.27 0.142 0.45 0.046 0.33 0.164 0.35 0.001 -0.46 0.001 4321 MMP12 -0.11 0.660 0.13 0.658 -0.14 0.460 0.46 0.052 0.77 0.000 0.26 0.010 -0.47 0.001 4322 MMP13 0.06 0.649 0.03 0.874 0.24 0.310 0.33 0.167 0.01 0.913 -0.19 0.158 4323 MMP14 -0.27 0.031 -0.29 0.120 0.30 0.187 0.33 0.163 0.19 0.070 -0.13 0.385 4324 MMP15 0.05 0.725 0.18 0.342 0.22 0.351 -0.06 0.811 0.28 0.009 -0.36 0.008 4325 MMP16 -0.02 0.857 0.34 0.067 0.40 0.081 -0.54 0.014 0.14 0.178 -0.39 0.006 4326 MMP17 0.14 0.342 -0.07 0.726 0.03 0.912 0.12 0.626 -0.08 0.474 4327 MMP19 -0.18 0.153 -0.34 0.064 0.23 0.328 -0.61 0.006 0.01 0.907 9313 MMP20 -0.25 0.376 -0.09 0.649 0.00 0.990 0.31 0.192 0.05 0.661 -0.15 0.306 8510 MMP23B -0.17 0.369 -0.24 0.306 0.11 0.651 -0.02 0.828 -0.03 0.827 10893 MMP24 0.01 0.964 -0.18 0.544 -0.32 0.083 -0.27 0.247 -0.50 0.028 0.19 0.081 64386 MMP25 -0.44 0.114 0.19 0.305 0.23 0.333 -0.02 0.952 56547 MMP26 -0.33 0.390 0.10 0.614 0.07 0.780 -0.03 0.905 64066 MMP27 -0.02 0.878 -0.02 0.915 0.56 0.011 0.25 0.329 79148 MMP28 0.15 0.442 -0.23 0.331 -0.45 0.055

5743 COX-2 -0.31 0.053 -0.14 0.443 0.21 0.275 -0.10 0.709 -0.13 0.606 0.26 0.024 -0.09 0.194 Shaded areas indicate statistically significant correlations by Pearson analysis. * For identification of datasets, see Table 1.

1 Supplemental Table 2b. Pearson correlation analysis of each randomly picked gene with OPN expression profiles. Dataset* IIIIII IV V VI VII ID GeneSymbol r P r P r P r P r P r P r P 321 APBA2 -0.07 0.664 0.15 0.447 0.10 0.123 -0.07 0.789 0.70 0.001 0.13 0.097 0.01 0.937 377 ARF3 0.17 0.327 0.12 0.518 -0.73 0.000 -0.12 0.675 0.17 0.472 0.31 0.005 -0.07 0.212 8703 B4GALT3 0.30 0.065 -0.22 0.247 -0.70 0.000 -0.34 0.148 0.03 0.908 0.26 0.035 -0.24 0.084 657 BMPR1A -0.24 0.151 -0.33 0.074 -0.61 0.000 0.32 0.119 -0.50 0.030 0.18 0.116 0.49 0.000 928 CD9 0.08 0.647 0.07 0.717 -0.54 0.003 0.08 0.704 -0.73 0.000 0.15 0.118 0.23 0.094 1105 CHD1 -0.06 0.739 0.61 0.001 -0.64 0.000 0.14 0.552 -0.08 0.745 -0.22 0.029 0.09 0.544 1649 DDIT3 0.02 0.921 0.20 0.305 -0.25 0.091 -0.09 0.706 0.37 0.111 0.12 0.152 0.31 0.026 1798 DPAGT1 0.03 0.848 0.19 0.316 -0.74 0.000 -0.14 0.582 -0.57 0.011 0.04 0.728 0.14 0.337 2125 EVPL 0.15 0.370 -0.18 0.362 0.58 0.001 -0.04 0.858 -0.48 0.039 -0.18 0.057 -0.10 0.476 3553 IL1B 0.32 0.329 0.32 0.108 -0.08 0.719 0.18 0.423 -0.16 0.520 0.05 0.475 0.20 0.159 9858 KIAA0649 -0.25 0.129 0.17 0.388 -0.35 0.059 -0.13 0.570 0.60 0.005 0.10 0.348 -0.19 0.182 4085 MAD2L1 -0.18 0.260 0.11 0.567 -0.43 0.016 -0.13 0.506 0.74 0.001 -0.08 0.377 0.22 0.108 23118 MAP3K7IP2 0.03 0.842 0.04 0.821 -0.20 0.300 0.08 0.760 -0.42 0.068 0.01 0.933 0.18 0.184 4361 MRE11A -0.17 0.303 -0.15 0.414 -0.47 0.008 0.19 0.419 0.52 0.025 -0.15 0.127 0.30 0.029 4818 NKG7 0.72 0.020 0.85 0.000 0.23 0.069 -0.36 0.024 -0.28 0.164 -0.40 0.094 -0.29 0.000 55746 NUP133 -0.09 0.577 -0.25 0.198 -0.72 0.000 0.04 0.848 0.06 0.795 -0.27 0.007 0.25 0.049 8473 OGT -0.02 0.928 0.21 0.277 -0.68 0.000 0.05 0.786 0.09 0.707 0.04 0.624 0.11 0.433 26986 PABPC1 0.03 0.859 -0.56 0.001 0.18 0.107 -0.17 0.314 -0.01 0.970 0.44 0.053 0.45 0.000 5581 PRKCE -0.50 0.133 -0.12 0.515 -0.07 0.696 -0.09 0.755 0.06 0.817 -0.22 0.007 0.08 0.569 22929 SEPHS1 0.02 0.885 0.19 0.300 -0.08 0.692 -0.17 0.379 0.49 0.032 0.04 0.672 0.40 0.003 10915 TCERG1 0.28 0.087 0.01 0.947 0.00 0.991 -0.02 0.905 0.69 0.001 -0.01 0.934 0.04 0.848 7381 UQCRB -0.31 0.054 0.25 0.179 -0.06 0.768 0.34 0.142 0.27 0.264 -0.24 0.011 0.35 0.010 7405 UVRAG -0.31 0.053 -0.14 0.443 0.21 0.275 -0.10 0.709 -0.13 0.606 0.26 0.024 -0.09 0.194 Shaded areas indicate statistically significant correlations by Pearson analysis. * For identification of datasets, see Table 1.

2 Supplemental Table 3a. List of gene sets significantly enriched (shaded areas) in association to OPN in at least one gene expression dataset generated by oligo nucleotide microarray platform. GENESETS POSITIVELY ENRICHED WITH OPN IN DATASET: III IV V VI VII

N° NOM FDR NOM FDR NOM FDR NOM FDR NOM FDR NAME Source NES NES NES NES NES genes p-val q-val p-val q-val p-val q-val p-val q-val p-val q-val ANGIOGENESIS 109 S 0.81 0.7138 0.8930 1.56 0.0228 1.0000 1.29 0.1764 0.3501 CELL_CYCLE 89 S 1.68 0.0550 0.2288 1.79 0.0123 0.0944 2.09 0.0151 0.0263 CELL_PROLIFERATION 72 Rosenwald et al. 1.89 0.0076 0.0672 0.81 0.7330 1.0000 1.43 0.0334 0.3203 1.75 0.0000 0.1239 DNA_DAMAGE_SIGNALING_PATHWAY 94 S 1.36 0.1264 0.5941 1.62 0.0165 0.1580 1.33 0.0853 0.3487 ECM_MEMBRANE_CELL-CELL_ADHESION 88 S 0.73 0.8029 0.9670 0.68 0.8980 0.9737 1.30 0.1113 0.4426 1.55 0.0345 0.2028 GENES_CONSTITUTING_THE_PI3_KINASE_PREDICTOR 92 Potti et al. 1.40 0.2090 0.5758 1.78 0.0043 0.0581 2.12 0.0127 0.0274 HEDGEHOG_SIGNALING_PATHWAY__KEGG 39 K 1.13 0.2937 0.9573 0.66 0.9426 1.0000 1.61 0.0446 0.1609 1.11 0.3176 1.0000 HYPOXIA_SIGNALING_PATHWAY 45 S 1.19 0.2416 0.7823 1.32 0.1068 0.4590 2.00 0.0000 0.0491 0.91 0.5791 1.0000 METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450__KEGG 40 K 0.62 0.9030 1.0000 1.85 0.0250 0.0845 NITRIC_OXIDE 134 S 0.84 0.6558 1.0000 1.64 0.0075 0.1443 PPAR_SIGNALING_PATHWAY__KEGG 60 K 0.64 0.9509 0.9531 1.39 0.0390 1.0000 0.72 0.8947 1.0000 PROLIFERATION_SIGNATURE 50 Whitfield et al. 1.48 0.1637 0.4510 1.71 0.0104 0.0958 2.34 0.0000 0.0013 RECURRENCE_SCORE 16 Paik et al. 1.05 0.4041 0.7800 1.57 0.0271 0.1550 1.98 0.0041 0.0437 0.97 0.4733 1.0000 ROTTERDAM_SIGNATURE 62 Klijn et al. 1.47 0.0716 0.4331 0.96 0.5787 1.0000 1.67 0.0078 0.1143 0.95 0.5168 0.6004 1.10 0.3152 1.0000 SHEPARD_CELL_PROLIFERATION 194 Shepherd et al. 1.22 0.1274 0.7243 0.81 0.8165 0.9841 1.04 0.3695 0.7669 1.72 0.0000 0.1122 T-CELL_AND_B-CELL_ACTIVATION 53 S 1.37 0.1306 1.0000 1.74 0.0091 0.1148 TOLL-LIKE_RECEPTOR_SIGNALING_PATHWAY__KEGG 86 K 0.71 0.8741 0.9589 0.58 0.9752 0.9993 1.63 0.0234 0.1402 TOXICOLOGY_&_DRUG_RESISTANCE 70 S 0.84 0.7958 0.8865 1.33 0.0761 0.4825 1.37 0.0396 0.3300 TSP1_PATHWAY 7 S 0.73 0.8141 0.9825 0.94 0.5290 1.0000 1.50 0.0472 0.2300 0.51 0.9707 0.9810 TUMOR_METASTASIS 59 S 1.66 0.0303 0.2160 0.77 0.8696 1.0000 1.27 0.0860 0.4950 1.72 0.0028 0.1033 UNDERHILL_PROLIFERATION 13 Underhill et al. 1.55 0.0726 0.4131 1.58 0.0578 0.1611 1.68 0.0310 0.1229 VV_70GENE_SIGNATURE 70 van'tVeer et al. 1.58 0.0221 0.1876 1.10 0.3346 0.4765 In the table are reported number of genes present in each geneset extracted from the datasets and source (K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Normalized Enrichment Score (NES), Nominal P Value (NOM), False Discovery Rate (FDR). Statistical threshold: enrichment with either both normalized p value < 0.01 and FDR <0.25 or at least one of the two parameters below the selected value. Supplemental Table 3b. List of gene sets significantly enriched (shaded areas) in association to MMP-9 in at least one gene expression dataset generated by oligo nucleotide microarray platform. GENESETS POSITIVELY ENRICHED WITH MMP9 IN DATASET: III IV V VI VII

N° NOM FDR NOM FDR NOM FDR NOM FDR NOM FDR NAME Source NES NES NES NES NES genes p-val q-val p-val q-val p-val q-val p-val q-val p-val q-val ANTIGEN_PROCESSING_AND_PRESENTATION__KEGG 69 K 1.39 0.0964 0.4616 0.81 0.7002 1.0000 0.99 0.4283 0.7587 2.09 0.0057 0.0071 APOPTOSIS 141 S 1.56 0.0229 0.4117 0.85 0.7555 1.0000 1.03 0.4075 0.7035 1.41 0.0433 0.2590 CELL_ADHESION_MOLECULES_(CAMS)_KEGG 89 K 1.52 0.0214 0.4111 0.75 0.7589 0.9690 2.10 0.0000 0.0128 CELL_PROLIFERATION 72 Rosenwald et al. 1.49 0.1680 0.3076 0.69 0.8787 1.0000 1.45 0.0231 0.4588 1.35 0.0708 0.2447 CHEMOKINE_LIGAND_RECEPTOR 90 S 1.21 0.2626 0.5539 0.90 0.5844 1.0000 0.86 0.6045 0.8052 1.84 0.0018 0.0298 DNA_DAMAGE_SIGNALING_PATHWAY 94 S 0.95 0.4833 0.5684 1.66 0.0108 0.2867 0.71 0.9220 0.8627 ECM_MEMBRANE_CELL-CELL_ADHESION 88 S 1.54 0.0122 0.4131 0.66 0.8863 1.0000 1.28 0.1232 0.4760 1.52 0.0422 0.1575 ECM_MEMBRANE_CELL-MATRIX_ADHESION 125 S 1.63 0.0236 0.3986 1.03 0.4220 0.7119 1.32 0.1049 0.2480 0.82 0.7348 1.0000 GENES_CONSTITUTING_THE_PI3_KINASE_PREDICTOR 92 Potti et al. 0.52 0.8686 0.9734 1.61 0.0124 0.2582 1.39 0.0942 0.2385 INFLAMMATORY_CYTOKINES_&_RECEPTORS 78 S 1.12 0.3911 0.4803 0.82 0.6498 1.0000 0.40 0.9870 1.0000 1.68 0.0128 0.0712 JAK___STAT_SIGNALING_PATHWAY 141 S 1.05 0.4246 0.5121 1.20 0.2677 1.0000 1.53 0.0123 0.1539 METALLOPROTEASES 24 S 1.04 0.4098 0.4891 1.20 0.2869 1.0000 1.10 0.3488 0.6847 1.73 0.0058 0.0525 NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY__KEGG 108 K 1.14 0.3532 0.4975 0.83 0.7348 1.0000 0.52 0.9874 1.0000 1.90 0.0000 0.0394 NFKB_SIGNALING_PATHWAY 87 S 0.99 0.5016 0.5404 0.72 0.8838 1.0000 1.58 0.0152 0.1232 NITROGEN_METABOLISM__KEGG 23 K 1.50 0.0417 0.3513 0.63 0.9119 0.0000 0.96 0.5363 0.7662 1.11 0.3145 0.9110 P53_SIGNALING_PATHWAY 105 S 1.25 0.1684 0.5690 1.72 0.0071 0.2576 0.80 0.8172 0.7765 PROLIFERATION_SIGNATURE 50 Whitfield et al. 1.51 0.0204 0.4818 1.82 0.0214 0.0292 RIBOSOME_KEGG 75 K 0.73 0.7169 0.8399 1.57 0.0448 1.0000 0.73 0.6378 0.9765 1.11 0.2884 0.9723 ROTTERDAM_SIGNATURE 62 Klijn et al. 1.30 0.2053 0.5489 1.38 0.0494 0.5073 0.87 0.6940 0.7108 0.95 0.5925 1.0000 SHEPARD_NEG_REG_OF_CELL_PROLIFERATION 103 Shepard et al. 1.48 0.0447 0.4900 1.02 0.4226 0.5716 SIGNAL_TRANSDUCTION_IN_CANCER 85 S 1.60 0.0637 0.3786 0.97 0.4537 0.7801 1.51 0.0494 0.1601 T-CELL_AND_B-CELL_ACTIVATION 53 S 1.22 0.2838 0.5691 0.85 0.6352 1.0000 0.40 1.0000 0.9958 2.02 0.0000 0.0131 T_CELL_RECEPTOR_SIGNALING_PATHWAY__KEGG 84 K 0.85 0.6447 0.6757 0.66 0.9268 1.0000 0.73 0.8767 0.9914 1.87 0.0000 0.0274 0.71 0.8919 0.9952 TNF_L&R 19 S 1.79 0.0316 0.2337 1.06 0.4220 1.0000 1.10 0.3478 0.7029 1.60 0.0356 0.1154 TOLL-LIKE_RECEPTOR_SIGNALING_PATHWAY__KEGG 86 K 0.96 0.5562 0.5591 0.61 0.9650 0.0000 0.53 0.9821 1.0000 1.70 0.0070 0.0666 TUMOR_METASTASIS 59 S 1.70 0.0390 0.3097 0.75 0.8613 1.0000 0.87 0.6864 0.8389 1.73 0.0000 0.0565 TUMOR_NECROSIS_FACTOR 61 S 1.12 0.2978 0.4732 1.07 0.3750 1.0000 1.33 0.0987 0.5137 1.87 0.0000 0.0320 0.68 0.9056 0.9870 UNDERHILL_PROLIFERATION 13 Underhill et al. 1.17 0.3231 0.5186 1.74 0.0071 0.4294 1.62 0.0184 0.1049 In the table are reported number of genes present in each geneset extracted from the datasets and source (K=KEGG, S=www.superarray.com, Rosenwald et al. Cancer Cell. 2003 Feb;3(2):185-97, Potti et al. Nat Med. 2006 Nov;12(11):1294-300, Whitfield et al. Mol Biol Cell. 2002 Jun;13(6):1977-2000, Paik et al. N Engl J Med. 2004 Dec 30;351(27):2817-26, Klijn et al. J Clin Oncol. 2006 Apr 10;24(11):1665-71, Shepard et al. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13194-9, Underhill et al. Blood. 2003 May 15;101(10):4013-21, van't Veer et al. Nature. 2002 Jan 31;415(6871):530-6. Normalized Enrichment Score (NES), Nominal P Value (NOM), False Discovery Rate (FDR). Statistical threshold: enrichment with either both normalized p value < 0.01 and FDR <0.25 or at least one of the two parameters below the selected value. Supplemental Table 4a. List of genes from the CELL_PROLIFERATION gene sets and their association with OPN and MMP-9 in datasets III, V and VI. Symbol Name OPN MMP9 ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) BUB3 BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) CDK6 Cyclin-dependent kinase 6 CDK7 Cyclin-dependent kinase 7 CKS1B CDC28 protein kinase regulatory subunit 1B CKS2 CDC28 protein kinase regulatory subunit 2 CSF1R Colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog EGFR Epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) EHF Ets homologous factor ELF5 E74-like factor 5 (ets domain transcription factor) EMP2 In multiple clusters EPHB4 EPH receptor B4 EVI5 Ecotropic viral integration site 5 FGF6 Fibroblast growth factor 6 FSCN1 Fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) FZD3 Frizzled homolog 3 (Drosophila) GAB1 GRB2-associated binding protein 1 GPC4 Glypican 4 GSPT1 G1 to S phase transition 1 HDGF Hepatoma-derived growth factor (high-mobility group protein 1-like) HDGFRP3 Hepatoma-derived growth factor, related protein 3 IL1A Interleukin 1, alpha IL1B Interleukin 1, beta IL2RG Interleukin 2 receptor, gamma (severe combined immunodeficiency) IL3 Interleukin 3 (colony-stimulating factor, multiple) IL6 Interleukin 6 (interferon, beta 2) IL6R Interleukin 6 receptor ISG20 Interferon stimulated exonuclease gene 20kDa KHDRBS1 KH domain containing, RNA binding, signal transduction associated 1 KIF2C Kinesin family member 2C KITLG KIT ligand KRT16 Keratin 16 (focal non-epidermolytic palmoplantar keratoderma) LGI1 Leucine-rich, glioma inactivated 1 MAD1L1 MAD1 mitotic arrest deficient-like 1 (yeast) MET Met proto-oncogene (hepatocyte growth factor receptor) MIA Melanoma inhibitory activity MNAT1 Menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis) MS4A1 Membrane-spanning 4-domains, subfamily A, member 1 MT3 Metallothionein 3 MTCP1 Mature T-cell proliferation 1 MYC Similar to ORF 114 NDP Norrie disease (pseudoglioma) NR6A1 Nuclear receptor subfamily 6, group A, member 1 NUDC Nuclear distribution gene C homolog (A. nidulans) PCNA Proliferating cell nuclear antigen PDAP1 PDGFA associated protein 1 PDGFA Platelet-derived growth factor alpha polypeptide PDZK1 PDZ domain containing 1 PIM2 Pim-2 oncogene PRDX1 Peroxiredoxin 1 PRG4 Proteoglycan 4 PRL Prolactin PTHLH Parathyroid hormone-like hormone PYY Peptide YY RBBP7 Retinoblastoma binding protein 7 RPS4X Ribosomal protein S4, X-linked SFN Stratifin SIPA1 Signal-induced proliferation-associated gene 1 SKP2 S-phase kinase-associated protein 2 (p45) TACSTD2 Tumor-associated calcium signal transducer 2 TAL1 T-cell acute lymphocytic leukemia 1 TFDP1 Transcription factor Dp-1 TGFA Transforming growth factor, alpha Thrombopoietin (myeloproliferative leukemia virus oncogene ligand, megakaryocyte growth and development THPO factor) TM4SF1 Transmembrane 4 L six family member 1 TNFRSF9 Tumor necrosis factor receptor superfamily, member 9 TNFSF8 Tumor necrosis factor (ligand) superfamily, member 8 TNFSF9 Tumor necrosis factor (ligand) superfamily, member 9 TPX2 TPX2, microtubule-associated, homolog (Xenopus laevis) ZFP36L2 Zinc finger protein 36, C3H type-like 2 Shaded areas indicate statistically significant enrichment

Supplemental Table 4b. List of genes from the GENES_CONSTITUTING_THE_PI3_KINASE_PREDICTOR gene sets and their association with OPN and MMP-9 in datasets III, V and VI. Symbol Name OPN MMP9 AKR7A3 Aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) ANKRD32 Ankyrin repeat domain 32 ATAD2 ATPase family, AAA domain containing 2 BARD1 BRCA1 associated RING domain 1 BRD2 Bromodomain containing 2 CASP8AP2 CASP8 associated protein 2 CDC45L CDC45 cell division cycle 45-like (S. cerevisiae) CDC25A Cell division cycle 25 homolog A (S. pombe) CDC6 Cell division cycle 6 homolog (S. cerevisiae) CDC7 Cell division cycle 7 homolog (S. cerevisiae) CDCA5 Cell division cycle associated 5 CDCA7 Cell division cycle associated 7 CHEK1 CHK1 checkpoint homolog (S. pombe) CSPG5 Chondroitin sulfate proteoglycan 5 (neuroglycan C) CDT1 Chromatin licensing and DNA replication factor 1 CSE1L CSE1 chromosome segregation 1-like (yeast) CCNE1 Cyclin E1 CCNE2 Cyclin E2 DDX10 DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 DNMT1 DNA (cytosine-5-)-methyltransferase 1 DCLRE1B DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae) EGR1 Early growth response 1 EED Embryonic ectoderm development FEN1 Flap structure-specific endonuclease 1 GPR27 G protein-coupled receptor 27 GAL Galanin prepropeptide GEMIN4 Gem (nuclear organelle) associated protein 4 GMNN Geminin, DNA replication inhibitor GADD45B Growth arrest and DNA-damage-inducible, beta GAS2L1 Growth arrest-specific 2 like 1 H2AFX H2A histone family, member X HSPA1A Heat shock 70kDa protein 1A HSPA1B Heat shock 70kDa protein 1B ID1 Inhibitor of DNA binding 1, dominant negative helix-loop-helix protein ITPKC Inositol 1,4,5-trisphosphate 3-kinase C IL17RB Interleukin 17 receptor B IL17D Interleukin 17D JUNB Jun B proto-oncogene JUN Jun oncogene JPH1 Junctophilin 1 LMNB1 Lamin B1 LMNB2 Lamin B2 LEF1 Lymphoid enhancer-binding factor 1 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) MTHFD1 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) MCM10 Minichromosome maintenance complex component 10 MCM2 Minichromosome maintenance complex component 2 MCM3 Minichromosome maintenance complex component 3 MCM4 Minichromosome maintenance complex component 4 MCM5 Minichromosome maintenance complex component 5 MCM6 Minichromosome maintenance complex component 6 MCM7 Minichromosome maintenance complex component 7 MSH2 MutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) NASP Nuclear autoantigenic sperm protein (histone-binding) NOL5A Nucleolar protein 5A (56kDa with KKE/D repeat) PEX5 Peroxisomal biogenesis factor 5 PPAT Phosphoribosyl pyrophosphate amidotransferase PRPS1 Phosphoribosyl pyrophosphate synthetase 1 KCTD12 Potassium channel tetramerisation domain containing 12 PRIM1 Primase, DNA, polypeptide 1 (49kDa) PCNA Proliferating cell nuclear antigen PRKRIR Protein-kinase, interferon-inducible double stranded RNA dependent inhibitor PDXP Pyridoxal (pyridoxine, vitamin B6) phosphatase RAD51 RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) RHOB Ras homolog gene family, member B RFC2 Replication factor C (activator 1) 2, 40kDa RFC3 Replication factor C (activator 1) 3, 38kDa RPA3 Replication protein A3, 14kDa RPP25 Ribonuclease P/MRP 25kDa subunit RRM2 Ribonucleotide reductase M2 polypeptide RBM15 RNA binding motif protein 15 SLC25A15 Solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 SLC25A19 Solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19 SPEN Spen homolog, transcriptional regulator (Drosophila) SLBP Stem-loop binding protein SUPT16H Suppressor of Ty 16 homolog (S. cerevisiae) SSX2IP Synovial sarcoma, X breakpoint 2 interacting protein TAF5 TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa TOP3A Topoisomerase (DNA) III alpha TCF19 Transcription factor 19 (SC1) TLE3 Transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila) TBRG4 Transforming growth factor beta regulator 4 TMEM18 Transmembrane protein 18 UBE2T Ubiquitin-conjugating enzyme E2T (putative) UHRF1 Ubiquitin-like, containing PHD and RING finger domains, 1 UNG Uracil-DNA glycosylase UMPS Uridine monophosphate synthetase MYB V-myb myeloblastosis viral oncogene homolog (avian) ZNF45 Zinc finger protein 45 ZNF473 Zinc finger protein 473 ZMYND19 Zinc finger, MYND-type containing 19 ZWINT ZW10 interactor antisense Shaded areas indicate statistically significant enrichment Supplemental Table 4c. List of genes from the PROLIFERATION_SIGNATURE gene sets and their association with OPN and MMP-9 in datasets III, V and VI. Symbol Name OPN MMP9 AURKB Aurora kinase B BIRC5 Effector cell peptidase receptor 1 BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) CCNA2 Cyclin A2 CCNB1 Cyclin B1 CCNE1 Cyclin E1 CCNE2 Cyclin E2 CCNF Cyclin F CDC20 Cell division cycle 20 homolog (S. cerevisiae) CDC25C Cell division cycle 25 homolog C (S. pombe) CDC6 Cell division cycle 6 homolog (S. cerevisiae) CDC7 Cell division cycle 7 homolog (S. cerevisiae) CDH3 Cadherin 3, type 1, P-cadherin (placental) CENPE Centromere protein E, 312kDa CENPF Centromere protein F, 350/400ka (mitosin) CHEK1 CHK1 checkpoint homolog (S. pombe) CKS2 CDC28 protein kinase regulatory subunit 2 CTPS CTP synthase DDX11 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like helicase homolog, S. cerevisiae) DHFR Dihydrofolate Reductase DNMT1 DNA (cytosine-5-)-methyltransferase 1 E2F3 E2F transcription factor 3 EGFR Epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) ERBB2 V-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) EXOSC9 Exosome component 9 FEN1 Flap structure-specific endonuclease 1 KRT5 Keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types) MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) MAPK13 Mitogen-activated protein kinase 13 MCM3 Minichromosome maintenance complex component 3 MCM4 Minichromosome maintenance complex component 4 MCM5 Minichromosome maintenance complex component 5 MCM6 Minichromosome maintenance complex component 6 MKI67 Antigen identified by monoclonal antibody Ki-67 MYB V-myb myeloblastosis viral oncogene homolog (avian) NASP Nuclear autoantigenic sperm protein (histone-binding) ORC1L Origin recognition complex, subunit 1-like (yeast) PCNA Proliferating cell nuclear antigen PKMYT1 Protein kinase, membrane associated tyrosine/threonine 1 PLK1 Polo-like kinase 1 (Drosophila) PRIM1 Primase, DNA, polypeptide 1 (49kDa) PTTG1 Pituitary tumor-transforming 1 RFC1 Replication factor C (activator 1) 1, 145kDa RRM1 Ribonucleotide reductase M1 RRM2 Ribonucleotide reductase M2 polypeptide TIMP1 TIMP metallopeptidase inhibitor 1 TOP2A Topoisomerase (DNA) II alpha 170kDa TP53 Tumor protein p53 TYMS Thymidylate synthetase UNG Uracil-DNA glycosylase Shaded areas indicate statistically significant enrichment Supplemental Table 4d. List of genes from the TUMOR_METASTASIS gene sets and their association with OPN and MMP-9 in datasets III, V and VI. Symbol Name OPN MMP9 APC Adenomatous polyposis coli BAI1 Brain-specific angiogenesis inhibitor 1 BRMS1 Breast cancer metastasis suppressor 1 CAV1 Caveolin 1, caveolae protein, 22kDa CD44 CD44 molecule (Indian blood group) CDK4 Cyclin-dependent kinase 4 CDKN2A Cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) CHD4 Chromodomain helicase DNA binding protein 4 CST7 Cystatin F (leukocystatin) CTNNA1 Catenin (cadherin-associated protein), alpha 1, 102kDa CTNNB1 Catenin (cadherin-associated protein), beta 1, 88kDa CXCL12 Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) CXCR4 Chemokine (C-X-C motif) receptor 4 DENR Density-regulated protein ETV4 Ets variant gene 4 (E1A enhancer binding protein, E1AF) ETV6 Ets variant gene 6 (TEL oncogene) EWSR1 Ewing sarcoma breakpoint region 1 FGFR4 Fibroblast growth factor receptor 4 FLT4 Fms-related tyrosine kinase 4 FN1 Fibronectin 1 GNRH1 Gonadotropin-releasing hormone 1 (luteinizing-releasing hormone) GNRH2 Gonadotropin-releasing hormone 2 GZMA Granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) HDAC1 Histone deacetylase 1 HPSE Heparanase HRAS V-Ha-ras Harvey rat sarcoma viral oncogene homolog HTATIP2 HIV-1 Tat interactive protein 2, 30kDa IL18 Interleukin 18 (interferon-gamma-inducing factor) IL1B Interleukin 1, beta IL8RB Interleukin 8 receptor, beta ITGA7 Integrin alpha 7 KISS1 KiSS-1 metastasis-suppressor MDM2 Mdm2 p53 binding protein homolog (mouse) MET Met proto-oncogene (hepatocyte growth factor receptor) METAP2 Methionyl aminopeptidase 2 MMP10 Matrix metallopeptidase 10 (stromelysin 2) MMP11 Matrix metallopeptidase 11 (stromelysin 3) MMP13 Matrix metallopeptidase 13 (collagenase 3) MMP7 Matrix metallopeptidase 7 (matrilysin, uterine) MMP9 Matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) MTA1 Metastasis associated 1 MTA2 Metastasis associated 1 family, member 2 MTSS1 Metastasis suppressor 1 MYB V-myb myeloblastosis viral oncogene homolog (avian) MYC Similar to ORF 114 MYCL1 V-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) NF2 Neurofibromin 2 (merlin) NME1 Non-metastatic cells 1, protein (NM23A) expressed in NME4 Non-metastatic cells 4, protein expressed in NR4A3 Nuclear receptor subfamily 4, group A, member 3 PCOLN3 Chromatin modifying protein 1A PLAUR Plasminogen activator, urokinase receptor PTHLH Parathyroid hormone-like hormone PTP4A3 Protein tyrosine phosphatase type IVA, member 3 RB1 Retinoblastoma 1 (including osteosarcoma) RHOC Ras homolog gene family, member C RORB RAR-related orphan receptor B S100A4 S100 calcium binding protein A4 SERPINB5 Serpin peptidase inhibitor, clade B (ovalbumin), member 5 Shaded areas indicate statistically significant enrichment