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Table 3 Hub genes among the aberrantly methylated differentially expressed genes ranked in cytoHubba

From: Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics

Category

Rank method in cytoHubba

Top 30 genes

Hypomethylated with high expression

Betweenness

AKT1, PRDM10, ACACA, GNB1, DICER1, CTBP1, ACTG1, CREBBP, HSP90AB1, DCY7, GNG7, PXN, POLR2D, PPP3CA, EEF2, BGN, GNB2, EHMT2, FASN, CCND1 , OXA1L, SHMT2, CBLB, ATP5B, UBE4A, RPL6, SYNJ2, TCF7L2, EPHB2, FAF2

Bottleneck

AKT1, PRDM10 , ACACA, DICER1, GNB1, ADCY7, CTBP1, SH3RF1, EHMT2, CREBBP, PPP3CA, ACTG1, FASN , RPL6, JUP, OXA1L, BGN, HSP90AB1, PXN, ECHS1, ATP5B, GPT2, POLR2D, CCND1 , SYNJ2, SHMT2, EIF4A1, USP7, CHEK1, EEF2

Closeness

AKT1, PRDM10, ACACA, GNB1, CCND1 , CTBP1, GNG7, DICER1, CREBBP, ADCY7, GNB2, PXN, IGF1R, PPP3CA, HSP90AB1, LEF1, EIF4A1, PDPK1, ITPR3, RPTOR, EHMT2, CHEK1, ACTG1, POLR2D, YWHAG, TCF7L2, EEF2, FASN , EPHB2, POLR3A

Radiality

AKT1, PRDM10 , ACACA, CCND1, CTBP1, DICER1, CREBBP, PPP3CA, IGF1R, GNB1, ADCY7, LEF1, PXN, EIF4A1, GNB2, HSP90AB1, GNG7, RPTOR, ITPR3, YWHAG, PDPK1, CHEK1, EHMT2, ACTG1, CASP8, TJP1, FASN , TSC2, EPHB2, TCF7L2

Stress

AKT1, PRDM10 , ACACA, GNB1, DICER1, CTBP1, ADCY7, GNG7, HSP90AB1, CREBBP, ACTG1, GNB2, POLR2D, PPP3CA, PXN, CBLB, EEF2, CCND1 , EHMT2, BGN, TCF7L2, UBE4A, ATP5B, IGF1R, SYNJ2, POLR3A, FASN , SHMT2, EIF4A1, CHEK1

Hypermethylated with low expression

Betweenness

CTNNB1, DPYD, FGF2, VCAM1, PTEN, KIT, CFTR, RHOB, DCN, KDR, DMD, ANXA2, PRKCB , PRKG2, DES, FLNA , FST, KAT2B, PIK3R1, ITGA1, FOXO1, TPM1, PDE4D, ACSS3, CCK, KITLG, NT5E, CUL1, GATA3, HOPX

Closeness

CTNNB1, FGF2, PTEN, KIT, VCAM1, KDR, PIK3R1, FOXO1, KITLG, DPYD, PROM1, CDKN1B, RHOB, LEPR, GJA1, PRKCB , KAT2B, ANXA2, DCN, SNAI2, DES, FGFR2, ITGA1, CUL1, FLNA , NT5E, CFTR, CCK, ANGPT1, PRKG2

Degree

CTNNB1, FGF2, PTEN,KIT, VCAM1, KDR, KITLG, PIK3R1, KAT2B, CUL1, DPYD, RHOB, FOXO1, FLNA , CDKN1B, DES, DCN, PRKCB, ITGA1, DMD, CCK, CFTR, ANXA2, PROM1, UBE3A, TPM1, PRKG2, NT5E, LEPR, FGFR2

Eccentricity

VCAM1, ANXA2, KIT, FGF2, KDR, PIK3R1, DMD, GJA1, PRKCB, PRKG2, TMOD1, ITGA1, COCH, CCK, AVPR1A, MTUS1, EDNRA, MYOF, FLNA, CFTR, CXCL1, LPAR1, ANXA6, GSN, PDE4D, NT5E, COL4A6, HLA-F, TRIM29, DAB1

Edge percolated component (EPC)

FGF2, CTNNB1, KIT, PTEN, KDR, VCAM1, KITLG, PIK3R1, PROM1, CDKN1B, FOXO1, CUL1, KAT2B, ITGA1, FGFR2, ANGPT1, GJA1, DES, SNAI2, RHOB, UBE3A, FLNA, PRKCB , CCK, LEPR, CUL2, NT5E, TNS1, DCN, ANXA2

  1. The italics are hub oncogenes and TSGs