Evolution of Network Biomarkers from Early to Late Stage Bladder Cancer Samples

Table 4

(a) The pathways analysis for 152 early stage significant proteins in carcinogenesis. (b) The pathway analysis and gene set enrichment analysis of the top 20 proteins of early stage bladder cancer on () biological processes, () cellular components, and () molecular functions by NOA.

(a)

Rank	Term	Count	Symbol	P value
1	hsa04110:Cell cycle	13	YWHAZ, CREBBP, TP53, PRKDC, RB1, CDK2, HDAC2, EP300, HDAC1, PCNA, MDM2, MYC, andCUL1	1.50E − 14
2	hsa05200:Pathways in cancer	11	TRAF2, EP300, HDAC2, HDAC1, CREBBP, TP53, MDM2, RB1, MYC, CDK2, and CTNNB1	3.51E − 07
3	hsa05215:Prostate cancer	7	EP300, CREBBP, TP53, MDM2, RB1, CDK2, and CTNNB1	1.45E − 06
4	hsa05220:Chronic myeloid leukemia	6	HDAC2, HDAC1, TP53, MDM2, RB1, and MYC	1.32E − 05
5	hsa04310:Wnt signaling pathway	6	EP300, CREBBP, TP53, MYC, CUL1, and CTNNB1	3.78E − 04
6	hsa05222:Small cell lung cancer	5	TRAF2, TP53, RB1, MYC, and CDK2	4.04E − 04
7	hsa05219:Bladder cancer	4	TP53, MDM2, RB1, and MYC	7.24E − 04
8	hsa04330:Notch signaling pathway	4	EP300, HDAC2, HDAC1, and CREBBP	0.001008
9	hsa04520:Adherens junction	4	EP300, CREBBP, SRC, and CTNNB1	0.00418
10	hsa04350:TGF-beta signaling pathway	4	EP300, CREBBP, MYC, and CUL1	0.005889
11	hsa05016:Huntington's disease	5	EP300, HDAC2, HDAC1, CREBBP, and TP53	0.006736
12	hsa05216:Thyroid cancer	3	TP53, MYC, and CTNNB1	0.00676
13	hsa04120:Ubiquitin mediated proteolysis	4	CUL3, MDM2, BRCA1, and CUL1	0.020254
14	hsa05213:Endometrial cancer	3	TP53, MYC, and CTNNB1	0.020793
15	hsa05214:Glioma	3	TP53, MDM2, and RB1	0.029762
16	hsa04115:p53 signaling pathway	3	TP53, MDM2, and CDK2	0.034267
17	hsa05218:Melanoma	3	TP53, MDM2, and RB1	0.037091
18	hsa05210:Colorectal cancer	3	TP53, MYC, and CTNNB1	0.050311
19	hsa04210:Apoptosis	3	TRAF2, IRAK1, and TP53	0.053574
20	hsa03450:Non-homologous end-joining	2	XRCC6and PRKDC	0.05487
21	hsa04916:Melanogenesis	3	EP300, CREBBP, and CTNNB1	0.067353
22	hsa04114:Oocyte meiosis	3	YWHAZ, CDK2, and CUL1	0.080913
23	hsa04722:Neurotrophin signaling pathway	3	IRAK1, YWHAZ, and TP53	0.099295

The significant pathways via DAVID Bioinformatics database are selected for the 152 significant proteins in carcinogenesis. Black background indicates value > 0.05.

(b)

GO:term	value	Corrected value					Term name
() Biological processes
0044260	5.3E − 11	1.7E − 8	14791	19	3428	18	Cellular macromolecule metabolic process
0043170	7.3E − 10	2.4E − 7	14791	19	3975	18	Macromolecule metabolic process
0044237	3.6E − 8	1.2E − 5	14791	19	4963	18	Cellular metabolic process
0006414	1.4E − 7	4.7E − 5	14791	19	101	5	Translational elongation
0019538	1.0E − 6	3.2E − 4	14791	19	2528	13	Protein metabolic process
0008152	1.1E − 6	3.6E − 4	14791	19	6033	18	Metabolic process
0044238	1.7E − 6	5.6E − 4	14791	19	5258	17	Primary metabolic process
0016071	4.4E − 6	0.0014	14791	19	364	6	mRNA metabolic process
0044267	3.3E − 5	0.0110	14791	19	1883	10	Cellular protein metabolic process
0009987	1.2E − 4	0.0406	14791	19	9216	19	Cellular process
() Cellular components
0030529	7.9E − 10	7.8E − 8	16768	18	510	9	Ribonucleoprotein complex
0032991	1.8E − 7	1.8E − 5	16768	18	3312	14	Macromolecular complex
0043228	1.2E − 6	1.2E − 4	16768	18	2051	11	Non-membrane-bounded organelle
0043232	1.2E − 6	1.2E − 4	16768	18	2051	11	Intracellular non-membrane-bounded organelle
0005840	1.5E − 6	1.5E − 4	16768	18	196	5	Ribosome
0005829	2.0E − 6	2.0E − 4	16768	18	1269	9	Cytosol
0043229	8.3E − 6	8.2E − 4	16768	18	8759	18	Intracellular organelle
0043226	8.5E − 6	8.4E − 4	16768	18	8773	18	Organelle
0044445	1.7E − 5	0.0016	16768	18	150	4	Cytosolic part
0033279	2.8E − 4	0.0287	16768	18	123	3	Ribosomal subunit
() Molecular functions
0003735	1.0E − 6	1.1E − 4	15767	19	161	5	Structural constituent of ribosome
0003723	1.8E − 4	0.0193	15767	19	755	6	RNA binding
0005198	8.0E − 4	0.0825	15767	19	643	5	Structural molecule activity
0031625	0.0013	0.1360	15767	19	45	2	Ubiquitin protein ligase binding
0003678	0.0013	0.1360	15767	19	45	2	DNA helicase activity
0004535	0.0024	0.2480	15767	19	2	1	Poly(A)-specific ribonuclease activity
0033130	0.0048	0.4956	15767	19	4	1	Acetylcholine receptor binding
0008201	0.0079	0.8140	15767	19	112	2	Heparin binding
0030332	0.0096	0.9890	15767	19	8	1	Cyclin binding
0004386	0.0129	1	15767	19	145	2	Helicase 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.