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Identification of the
Bona fide
Differentially Methylated Gene Markers among Cancers
12
Table 1 Functional enrichment analysis for genes related with bona fide c-DMSs
Term
Genes
Cell-cell signaling
EREG
,
HTR2A
,
GRIA4
,
CCL20
,
KCNIP1
Defense response
DEFA1
,
DEFA6
,
ITGB6
,
CCL20
,
TNFRSF4
Cell adhesion
PGM5
,
DEFA6
,
ICAM4
,
MSLN
,
SIGLEC10
Biological adhesion
PGM5
,
ITGB6
,
ICAM4
,
MSLN
,
SIGLEC10
Cell proliferation
PDZK1
,
MT3
,
EREG
,
TNFRSF4
,
CCL20
Response to wounding
EREG
,
ITGB6
,
CCL20
,
TNFRSF4
Digestion
CAPN9
,
CAPN9
,
TFF2
Defense response to bacterium
DEFA1
,
DEFA6
,
CCL20
Response to bacterium
DEFA1
,
DEFA6
,
CCL20
Negative regulation of cell differentiation
MT3
,
EREG
,
DLL3
Positive regulation of multicellular organismal process
EREG
,
HTR2A
,
GRIA4
Defense response to fungus
DEFA1
,
DEFA6
Killing of cells of another organism
DEFA1
,
DEFA6
Regulation of synaptic transmission, glutamatergic
HTR2A
,
GRIA4
Cell killing
DEFA1
,
DEFA6
Response to fungus
DEFA1
,
DEFA6
Negative regulation of neurogenesis
MT3
,
DLL3
Negative regulation of cell development
MT3
,
DLL3
Note: Only annotations with p value < 0.05 for GO in all levels are listed here
Table 2 Functional enrichment analysis for Proteins/genes in protein interaction sub-network
Term
Gene Num.
p
value
Multicellular organismal process
152
5.01E-12
Homeostatic process
46
1.01E-09
Cell-cell signaling
44
1.14E-09
Response to chemical stimulus
81
1.36E-09
Regulation of multicellular organismal process
54
4.66E-09
Chemical homeostasis
34
1.64E-08
Response to stress
84
2.98E-08
Wound healing
31
6.02E-08
Response to wounding
42
1.49E-07
Ion homeostasis
27
2.40E-07
Developmental process
107
2.74E-07
Cell proliferation
48
4.31E-07
Cell differentiation
70
6.76E-07
Cell morphogenesis
32
1.36E-06
Localization of cell
29
2.08E-06
Cation homeostasis
20
4.47E-06
Regulation of sequence-specific DNA binding transcription factor activity
16
4.77E-06
Regulation of transcription regulator activity
16
5.84E-06
Response to stimulus
157
6.30E-06
Regulation of cell communication
39
6.88E-06
Protein modification process
65
8.71E-06
MAPKKK cascade
20
8.71E-06
Regulation of signaling
51
1.04E-05
Central nervous system development
26
1.48E-05
Immune system process
51
1.76E-05
Response to drug
18
1.78E-05
Small cell lung cancer
10
5.68E-05
MI:hsa-miR-323-5p
28
1.03E-04
Regulation of actin cytoskeleton
15
1.75E-04
Pathways in cancer
19
3.58E-04
Note: Only annotations with
p
value <0.05 for GO in all levels are listed here
Computational
Molecular Biology