Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

Table 2

Target genes found across methods.

Method	Target genes
CIPHER	ATM, BRCA1, CAV1, CCND1, CDKN1A, CDKN1B, EGFR, EGR1, ESR1, ESR2, HIF1A, HRAS, MME, MSH2, MYC, NCOA3, NCOA4, PGR, RB1, RNF14, SMARCA4, TP53
ENDEAVOUR	ACPP, ANXA7, APC, ARMET, ATM, BCL2, BMP6, BRCA1, BTRC, CAV1, CCND1, CD44, CDH1, CDH13, CDKN1A, CDKN1B, CDKN2A, CTCF, CTNNA1, CTNNB1, CYP1B1, DAPK1, EDNRB, EGFR, EGR1, ERBB2, ERCC5, ESR1, ESR2, FAF1, FHIT, GGT1, GSTP1, HIF1A, HOXA13, HRAS, IGFBP3, IL12A, IL8, KLK10, KLK2, KLK3, MAP2K4, MME, MSH2, MYC, NAT1, NCOA3, NCOA4, NEFL, PGK1, PGR, PLAU, POLB, PTPN13, RARB, RASSF1, RB1, RNF14, SLC2A2, SMARCA4, SOX2, STMN1, TCEB1, TMEPAI, TNF, TP53, TYR, VDR
ToppNet (K-Step Markov, HITS with Priors, PageRank with Priors	ACPP, ANXA7, APC, ATM, BCL2, BMP6, BRCA1, BTRC, CAV1, CCND1, CD44, CDH1, CDH13, CDKN1A, CDKN1B, CDKN2A, CTCF, CTNNA1, CTNNB1, CYP1B1, DAPK1, EDNRB, EGFR, EGR1, ERBB2, ERCC5, ESR1, ESR2, FAF1, FHIT, GGT1, GSTP1, HIF1A, HOXA13, HRAS, IGFBP3, IL12A, IL8, KLK10, KLK2, KLK3, MAP2K4, MC1R, MME, MSH2, MYC, NAT1, NCOA3, NCOA4, NEFL, NME1, PGK1, PGR, PLAU, POLB, PTPN13, RARB, RASSF1, RB1, RNF14, SLC2A2, SMARCA4, SOX2, STMN1, TCEB1, TNF, TP53, TYR, VDR
GP-MIDAS-VXEF	ACPP, ANXA7, APC, ARMET, ATM, BCL2, BMP6, BRCA1, BTRC, CAV1, CCND1, CD44, CDH1, CDH13, CDKN1A, CDKN1B, CDKN2A, CTCF, CTNNA1, CTNNB1, CYP1B1, DAPK1, EDNRB, EGFR, EGR1, EIF3S3, ERBB2, ERCC5, ESR1, ESR2, FAF1, FHIT, GGT1, GSTP1, HIF1A, HOXA13, HRAS, IGFBP3, IL12A, IL8, KLK10, KLK2, KLK3, MAP2K4, MC1R, MME, MSH2, MYC, NAT1, NCOA3, NCOA4, NEFL, NME1, PGK1, PGR, PLAU, POLB, PTPN13, RARB, RASSF1, RB1, RNF14, SLC2A2, SMARCA4, SOX2, STMN1, TCEB1, TMEPAI, TNF, TP53, TYR, VDR, VEGF