Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis

Table 1 Gene ontology enrichment analysis of methylation-regulated differentially expressed genes associated with colon cancer

Category	Term	Gene name	P-value
BP	GO:0045666-positive regulation of neuron differentiation	FEZF1, VWC2, NAP1L2, NKX2-5, BRINP3	4.08E-04
BP	GO:0007268-chemical synaptic transmission	DRD5, NOVA1, GRIA4, KCNA1, SNAP91, NPY, HTR7	7.08E-04
BP	GO:0006366-transcription from RNA polymerase II promoter	HAND1, FEV, PAX2, POU3F4, NKX2-5, IRF4, HAND2, PDX1, FOXF2	2.01E-03
BP	GO:0045944-positive regulation of transcription from RNA polymerase II promoter	HAND1, NR5A2, TBX5, PAX2, GDNF, NKX2-5, FOXD3, GALR1, IRF4, HAND2, PDX1, FOXF2	4.04E-03
BP	GO:0030154-cell differentiation	FEV, TLL1, COL19A1, NKX2-5, CHRDL1, SFRP5, SIM2, INA	4.52E-03
BP	GO:0045893-positive regulation of transcription, DNA-templated	FEZF1, NR5A2, TBX5, PAX2, NKX2-5, IRF4, HAND2, FOXF2	8.06E-03
BP	GO:0007189-adenylate cyclase-activating G-protein coupled receptor signaling pathway	ADRB3, DRD5, GALR1	2.10E-02
BP	GO:0051891-positive regulation of cardioblast differentiation	TBX5, NKX2-5	2.21E-02
BP	GO:0043433-negative regulation of sequence-specific DNA binding transcription factor activity	HAND1, SFRP5, HAND2	2.95E-02
BP	GO:0003337-mesenchymal to epithelial transition involved in metanephros morphogenesis	PAX2, GDNF	3.09E-02
BP	GO:0018108-peptidyl-tyrosine phosphorylation	EPHA7, EPHA6, RELN, EPHA5	3.11E-02
BP	GO:0008285-negative regulation of cell proliferation	FEZF1, TBX5, SFRP5, RERG, RIPPLY3, PDX1	3.20E-02
BP	GO:0000122-negative regulation of transcription from RNA polymerase II promoter	FEZF1, HAND1, NKX2-5, SIM2, RIPPLY3, DUSP26, FOXD3, PDX1	4.15E-02
BP	GO:0030509-BMP signaling pathway	BMP3, NKX2-5, CHRDL1	4.54E-02
CC	GO:0030425-dendrite	EPHA7, RELN, GRIA4, KCNA1, BRINP3, EPHA5, HTR7	4.25E-03
CC	GO:0090575-RNA polymerase II transcription factor complex	HAND1, NR5A2, NKX2-5	9.87E-03
CC	GO:0005578-proteinaceous extracellular matrix	RELN, COL19A1, CCBE1, EMILIN3, SPOCK3	3.40E-02
CC	GO:0044224-juxtaparanode region of axon	KCNA1, EPB41L3	4.46E-02
CC	GO:0005887-integral component of plasma membrane	JAM2, EPHA7, CALY, EPHA6, ADRB3, DRD5, GPR88, TMEM130, KCNA1, GALR1, EPHA5, HTR7	4.77E-02
MF	GO:0008134-transcription factor binding	HAND1, TBX5, PAX2, NKX2-5, IRF4, HAND2, PDX1, FOXF2	1.43E-04
MF	GO:0003700-transcription factor activity, sequence-specific DNA binding	DMRTA1, FEV, NR5A2, TBX5, POU3F4, NKX2-5, RXRG, SIM2, FOXD3, IRF4, PDX1, FOXF2	1.49E-03
MF	GO:0000977-RNA polymerase II regulatory region sequence-specific DNA binding	TBX5, POU3F4, RXRG, FOXD3, HAND2, FOXF2	1.50E-03
MF	GO:0043565-sequence-specific DNA binding	FEV, NR5A2, TBX5, NKX2-5, RXRG, IRX6, IRF4, FOXF2	4.74E-03
MF	GO:0044212-transcription regulatory region DNA binding	HAND1, NR5A2, PAX2, NKX2-5, HAND2	1.07E-02
MF	GO:0046982-protein heterodimerization activity	JAM2, HAND1, NKX2-5, SIM2, HAND2, PDX1, KHDRBS2	1.10E-02
MF	GO:0000978-RNA polymerase II core promoter proximal region sequence-specific DNA binding	FEZF1, HAND1, NR5A2, NKX2-5, IRF4, PDX1	1.41E-02
MF	GO:0005004-GPI-linked ephrin receptor activity	EPHA7, EPHA5	2.79E-02

BP: Biological process; CC: Cellular component; MF: Molecular function.

Table 2 Kyoto encyclopedia of genes and genomes pathway analysis of methylation-regulated differentially expressed genes associated with colon cancer

Pathway ID	Description	Gene name	P-value
hsa04970	Salivary secretion	CST2, ADRB3, ATP1B2, PRKG2	2.80e-04
hsa04923	Regulation of lipolysis in adipocytes	NPY, ADRB3, PRKG2	1.12e-03
hsa04080	Neuroactive ligand-receptor interaction	GRIA4, ADRB3, DRD5, GALR1, HTR7	2.59e-03
hsa04024	cAMP signaling pathway	NPY, GRIA4, DRD5, ATP1B2	4.95e-03
hsa04728	Dopaminergic synapse	GRIA4, DRD5, CALY	9.85e-03
hsa04978	Mineral absorption	MT1E, ATP1B2	1.41e-02
hsa05202	Transcriptional misregulation in cancer	FEZ, RXRG	2.05e-02
hsa04022	cGMP-PKG signaling pathway	ADRB3, ATP1B2, PRKG2	2.12e-02
hsa04360	Axon guidance	EPHA7, EPHA5, EPHA6	2.28e-02
hsa04020	Calcium signaling pathway	ADRB3, DRD5, HTR7	2.31e-02