Evolution of Network Biomarkers from Early to Late Stage Bladder Cancer Samples
Table 5
(a) The pathways analysis for 50 significant proteins in late stage bladder cancer carcinogenesis. (b) The pathway analysis and gene set enrichment analysis of the top 20 proteins of late stage bladder cancer on () biological processes, () cellular components and () molecular functions by NOA.
(a)
Rank
Term
Count
Symbol
P value
1
hsa03010:Ribosome
8
RPS28, RPS16, RPL22, RPL27, RPL12, RPS6, RPS8, and RPS23
2.26E − 07
2
hsa03040:Spliceosome
5
HSPA1L, CDC5L, SF3A1, SNRPE, and HNRNPU
0.004054716
3
hsa04120:Ubiquitin mediated proteolysis
4
CUL3, CUL5, BRCA1, and CUL1
0.034906958
The significant pathways via DAVID Bioinformatics database are selected for the 50 significant proteins in carcinogenesis.
(b)
GO:term
value
Corrected value
Term name
() Biological processes
GO:0045786
1.8E − 6
0.0010
14791
18
178
5
Negative regulation of cell cycle
GO:0022402
2.4E − 6
0.0014
14791
18
562
7
Cell cycle process
GO:0007050
8.4E − 6
0.0049
14791
18
111
4
Cell cycle arrest
GO:0051726
8.5E − 6
0.0049
14791
18
435
6
Regulation of cell cycle
GO:0060710
1.3E − 5
0.0080
14791
18
5
2
Chorioallantoic fusion
GO:0044260
1.4E − 5
0.0081
14791
18
3428
13
Cellular macromolecule metabolic process
GO:0051052
1.5E − 5
0.0091
14791
18
130
4
Regulation of DNA Metabolic process
GO:0008629
2.6E − 5
0.0155
14791
18
49
3
Induction of apoptosis by intracellular signals
GO:0006917
2.8E − 5
0.0162
14791
18
313
5
Induction of apoptosis
GO:0012502
2.8E − 5
0.0165
14791
18
314
5
Induction of programmed cell death
() Cellular components
GO:0032991
5.2E − 10
5.5E − 8
16768
18
3312
16
Macromolecular complex
GO:0005829
1.4E − 7
1.5E − 5
16768
18
1269
10
Cytosol
GO:0043234
2.5E − 6
2.6E − 4
16768
18
2748
12
Protein complex
GO:0005654
6.1E − 6
6.4E − 4
16768
18
465
6
Nucleoplasm
GO:0044428
6.4E − 5
0.0067
16768
18
1932
9
Nuclear part
GO:0000307
9.8E − 5
0.0102
16768
18
14
2
Cyclin-dependent protein kinase holoenzyme complex
GO:0030529
1.5E − 4
0.0163
16768
18
510
5
Ribonucleoprotein complex
GO:0031461
4.9E − 4
0.0516
16768
18
31
2
Cullin-RING ubiquitin ligase complex
GO:0022627
7.4E − 4
0.0777
16768
18
38
2
Cytosolic small ribosomal subunit
GO:0043626
0.0010
0.1116
16768
18
1
1
PCNA complex
() Molecular functions
GO:0019899
3.1E − 5
0.0037
15767
18
584
6
Enzyme binding
GO:0005515
1.1E − 4
0.0129
15767
18
8097
17
Protein binding
GO:0030337
0.0011
0.1335
15767
18
1
1
DNA polymerase processivity factor activity
GO:0000701
0.0011
0.1335
15767
18
1
1
Purine-specific mismatch base pair DNA N-glycosylase activity
GO:0031625
0.0011
0.1384
15767
18
45
2
Ubiquitin protein ligase binding
GO:0000166
0.0021
0.2510
15767
18
2283
8
Nucleotide binding
GO:0035033
0.0022
0.2669
15767
18
2
1
Histone deacetylase regulator activity
GO:0004696
0.0022
0.2669
15767
18
2
1
Glycogen synthase kinase 3 activity
GO:0000700
0.0022
0.2669
15767
18
2
1
Mismatch base pair DNA N-glycosylase activity
GO:0005200
0.0031
0.3705
15767
18
74
2
Structural constituent of cytoskeleton
: 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.