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Supplementary Data 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 MMP-9 activity MMP-9 (arbitrary(arbitrary units) 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
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