Table 3 Module analysis of the protein–protein interaction network
From: Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer
Category | Module | Function description | FDR | Nodes | Genes |
|---|---|---|---|---|---|
Hypomethylation and high expression | |||||
|  | 1 | Chemokine signaling pathway | 1.14E−10 | 6 | CCL18, CXCL2, CXCL1, CCL20, CXCL9, CXCL3 |
|  | 2 | Ribosome | 6.80E−04 | 5 | RPL31, PABPC1, UPF3A, RPS15A, RPS15 |
| Â | 3 | Nucleic acid binding | 0.0195 | 9 | DDX49, AHR, GSTP1, RB1, AATF, DDX56, NOC2L, IMP4, DDX52 |
|  | 4 | Carbon metabolism | 3.43E−04 | 5 | GNPDA1, PFKM, ENO1, ME1, HK3 |
|  | 5 | Cell cycle | 3.01E−10 | 8 | CDC16, PKMYT1, CDC27, TFDP1, SMARCAL1, ATM, RECQL5, WEE1 |
| Â | 6 | Proteasome | 0.0344 | 8 | FGFR1, SOX9, PSMD6, FOXD1, CCND1, MSX1, PSMF1, FOXA2 |
Hypermethylation and low expression | |||||
|  | 1 | Synaptic transmission | 1.04E−07 | 7 | KCND3, KCNG1, KCNB1, HCN2, KCNK3, KCNA5, KCNA3 |
|  | 2 | Gastric acid secretion | 2.19E−04 | 6 | SST, NPY, SSTR2, CCR10, PTGER3, ADCY2 |
|  | 3 | Glutamatergic synapse | 1.09E−06 | 5 | GRIK1, GRIK2, GRIA3, GRIN2A, CAMK2B |
|  | 4 | Cell fate specification | 9.20E−03 | 15 | ARHGEF16, RHOH, TIAM1, ABR, RAP1A, NEUROD1, AR, ESR1, EGFR, TF, FEV, INPP5B, SOX17, FGD2, NKX2-2 |