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Table 4 Module analysis of the protein–protein interaction network

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

Category

Module

Score

Nodes

Enrichment and pathway description

Genes

Hypomethylated with high expression

1

12.00

12

GO:0016874—ligase activity

GO:0004842—ubiquitin protein transferase activity

GO:0000209—protein polyubiquitination

hsa04120: ubiquitin-mediated proteolysis

GO:0071377—cellular response to glucagon stimulus

TRIM36, HERC3, NEDD4L, UBE4A, CBLB, SH3RF1, ASB13, MYLIP, RNF220, UBA1, UBE2H, RBBP6

2

10.00

10

GO:0007186—G-protein-coupled receptor signalling pathway

GO:0007193—adenylate cyclase-inhibiting G-protein-coupled receptor signalling pathway

hsa04727: GABAergic synapse

ADCY7, GNB1, GNB2, GNG7, ADCY1, DRD3, HTR1E, SST, RLN3, ADRA2A

3

8.889

10

GO:0005634—nucleus

GO:0005515—protein binding

GO:0006260—DNA replication

hsa04110: cell cycle

CENPF, E2F8, TK1, HJURP, MCM3, ZWINT, MELK, CDKN3, EXO1, CHEK1

4

7.00

7

GO:0030669—clathrin-coated endocytic vesicle membrane

GO:0060071—Wnt signalling pathway, planar cell polarity pathway

GO:0035615—clathrin adaptor activity

hsa04144: endocytosis

FZD4, REPS2, ADRB2, SYNJ2, AP2M1, AP2A2, AAK1

5

5.20

16

GO:0006383—transcription from RNA polymerase III promoter

GO:0003899—DNA-directed RNA polymerase activity

GO:0032481—positive regulation of type I interferon production

hsa00230: purine metabolism

POLR2D, GUCY2F, TCF7L2, POLR1D, EEF2, POLR3H, GUCY1A3, SNAPC4, TCEANC, JUP, WNT7B, CTBP1, DVL3, BRF1, CREBBP, POLR3A

6

3.444

19

GO:0001649—osteoblast differentiation

GO:0030206—chondroitin sulfate

GO:0005515—protein binding

hsa05222: focal adhesion

FHIT, COL4A1, DROSHA, NUMA1, DDX21, CMKLR1, COL3A1, DICER1, B3GALT6, OXA1L, MEF2D, FUS, DNMT3B, ARFIP2, VCAN, THBS2, CCND1, XYLT1, AKT1

7

3.143

8

GO:0009058—biosynthetic process

GO:0005759—mitochondrial matrix

GO:0030170—pyridoxal phosphate binding

hsa01230: biosynthesis of amino acids

GPT2, FASN, GOT2, RPTOR, ATP5B, TSC2, PRDM10, SHMT2

Hypermethylated with low expression

1

6.00

13

GO:0016032—viral process

GO:0048015—phosphatidylinositol-mediated signalling

GO:0061630—ubiquitin protein ligase activity

hsa05200: pathways in cancer

CUL2, PIK3R1, UBE3A, PTEN, PROM1, FBXL3, KITLG, KIT, KLHL2, FBXO17, CUL1, VCAM1, UBE2V2

2

3.667

7

GO:0007202—activation of phospholipase C activity

GO:0010595—positive regulation of endothelial cell migration

GO:0008284—positive regulation of cell proliferation

ANGPT1, FGF2, LPAR1, EDNRA, KDR, AVPR1A, CCK

3

3.333

7

hsa04015: Rap1 signalling pathway

GO:0045944—positive regulation of transcription from RNA

Polymerase II promoter

GO:0005654—nucleoplasm

HLA-F, IRF2, PPARGC1A, TRIM29, CDK8, CEBPB, KAT2B