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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
  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
  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