Applying NGS Data to Find Evolutionary Network Biomarkers from the Early and Late Stages of Hepatocellular Carcinoma
Table 6
(a) The pathways analysis for 74 significant proteins in the total stage carcinogenesis. (b) The pathway analysis and gene set enrichment analysis of the 74 proteins of total-stage liver cancer on () biological processes, () cellular components, and () molecular functions by NOA.
h_p27Pathway:Regulation of p27 Phosphorylation during Cell Cycle Progression
3
E2F1, NEDD8, CDK2
0.020162
3a
h_p53Pathway:p53 Signaling Pathway
3
E2F1, PCNA, CDK2
0.033691
4a
h_her2Pathway:Role of ERBB2 in Signal Transduction and Oncology
3
GRB2, MAPK3, ESR1
0.049866
5a
h_ptenPathway:PTEN dependent cell cycle arrest and apoptosis
3
GRB2, MAPK3, PTEN
0.054277
6a
h_RacCycDPathway:Influence of Ras and Rho proteins on G1 to S Transition
3
E2F1, MAPK3, CDK2
0.063496
7a
h_cellcyclePathway:Cyclins and Cell Cycle Regulation
3
E2F1, CDK1, CDK2
0.068295
The significant pathways via DAVID Bioinformatics database are selected for the 74 significant proteins in carcinogenesis. Bold indicates value > 0.05. Most of them are from the KEGG database, and we add several key pathways from BioCarta.
(b)
GO:term
value
Corrected value
Term name
() Biological processes
GO:0051320
6357
9
12
4
S phase
GO:0000084
6357
9
12
4
S phase of mitotic cell cycle
GO:0006267
6357
9
16
4
Prereplicative complex assembly
GO:0065004
6357
9
68
5
Protein-DNA complex assembly
GO:0000727
6357
9
26
4
Double-strand break repair via break-induced replication
GO:0006270
6357
9
28
4
DNA-dependent DNA replication initiation
GO:0022616
6357
9
31
4
DNA strand elongation
GO:0006271
6357
9
31
4
DNA strand elongation involved in DNA replication
GO:0000724
6357
9
38
4
Double-strand break repair via homologous recombination
GO:0022402
6357
9
445
7
Cell cycle process
() Cellular components
GO:0042555
6357
9
6
4
MCM complex
GO:0005656
6357
9
16
4
Prereplicative complex
GO:0031261
6357
9
22
4
DNA replication preinitiation complex
GO:0031298
6357
9
25
4
Replication fork protection complex
GO:0032993
6357
9
46
4
Protein-DNA complex
GO:0043234
6357
9
1369
9
Protein complex
GO:0044454
6357
9
217
5
Nuclear chromosome part
GO:0044451
6357
9
275
5
Nucleoplasm part
GO:0044428
6357
9
1251
8
Nuclear part
GO:0044427
0.0011
6357
9
302
5
Chromosomal part
() Molecular functions
GO:0043566
6357
9
85
6
Structure-specific DNA binding
GO:0043138
6357
9
18
4
3′-5′ DNA helicase activity
GO:0004003
6357
9
26
4
ATP-dependent DNA helicase activity
GO:0003682
6357
9
80
5
Chromatin binding
GO:0003688
6357
9
30
4
DNA replication origin binding
GO:0003678
6357
9
39
4
DNA helicase activity
GO:0003697
6357
9
44
4
Single-stranded DNA binding
GO:0016887
6357
9
278
6
ATPase activity
GO:0043140
6357
9
13
3
ATP-dependent 3′-5′ DNA helicase activity
GO:0008094
6357
9
67
4
DNA-dependent ATPase activity
: number of genes in reference set. : number of genes in test set. : number of genes annotated by given term in reference set. : number of genes annotated by given term in test set.