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.