Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

Dopazo, Joaquin; Erten, Cesim

doi:10.1186/s12918-017-0495-0

BMC Systems Biology

Table 3 Top 50 genes with respect to M _bw

From: Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

	Id	Gene	W _bw	N	T	M	G S ₁	G S ₂	Top neighbors in MWIS
1	Q15796	SMAD2	0.896534	64	31	0	Yes	Yes
2	Q14164	IKBKE	0.646178	1	16	0	No	No
3	P54274	TERF1	0.638236	59	55	0	No	No	1, 20, 34
4	P68400	CSNK2A1	0.626417	85	91	0	No	No
5	P04637	TP53	0.60796	98	97	17	Yes	Yes	1, 4, 7, 8, 34, 42, 44
6	Q99750	MDFI	0.60268	60	36	0	No	No
7	P04183	TK1	0.578819	10	92	0	No	No
8	Q96SB4	SRPK1	0.457947	0	36	0	No	No
9	Q13526	PIN1	0.438312	68	77	0	No	No	4, 6, 46
10	P46108	CRK	0.297179	96	70	0	No	No	21, 25, 35
11	P62993	GRB2	0.284621	97	98	0	No	No	2, 46
12	Q99558	MAP3K14	0.283214	45	17	0	No	No
13	Q9Y6K9	IKBKG	0.271303	4	10	0	No	No	12, 19
14	Q13387	MAPK8IP2	0.269689	1	60	0	No	No
15	Q13233	MAP3K1	0.255928	68	63	4	No	Yes
16	Q09472	EP300	0.250913	94	89	0	Yes	Yes	1, 34, 35
17	P21246	PTN	0.248842	53	2	0	No	No
18	P20333	TNFRSF1B	0.234258	71	31	0	No	No
19	Q99759	MAP3K3	0.233384	19	4	0	No	No
20	O60341	KDM1A	0.229576	79	93	0	No	No
21	Q92569	PIK3R3	0.225153	29	76	0	No	No
22	Q15714	TSC22D1	0.22131	99	76	0	No	No	17, 42
23	Q92624	APPBP2	0.217109	41	38	0	No	No	2
24	Q15047	SETDB1	0.212244	81	95	0	No	No	7, 20
25	P30480	HLA-B	0.20772	99	99	0	No	No
26	P25791	LMO2	0.197168	38	2	0	No	Yes
27	P25786	PSMA1	0.194226	4	36	0	No	No	2, 25, 40
28	P08238	HSP90AB1	0.187144	99	99	0	No	No	2, 4, 8, 12, 15, 19, 34, 42, 49
29	P14921	ETS1	0.184287	82	42	0	No	No
30	P12757	SKIL	0.177551	32	73	1	No	No	1
31	P03372	ESR1	0.175797	4	36	0	Yes	Yes	15
32	Q16539	MAPK14	0.173795	60	33	0	No	No	8
33	P63104	YWHAZ	0.172695	99	99	0	No	No	7, 19, 42
34	P22736	NR4A1	0.170823	84	44	0	No	No
35	O15162	PLSCR1	0.169279	90	76	0	No	No
36	P12931	SRC	0.169016	4	28	0	No	Yes	4, 21
37	P04626	ERBB2	0.164884	88	98	1	No	Yes	8, 14, 21
38	P40337	VHL	0.158704	99	99	0	No	Yes	6
39	Q96EB6	SIRT1	0.153643	94	68	1	Yes	No	4
40	P40692	MLH1	0.147726	1	20	0	No	Yes
41	Q9Y4K3	TRAF6	0.145986	2	2	0	No	No	12, 19
42	P04792	HSPB1	0.14386	99	99	0	No	No
43	Q5UIP0	RIF1	0.139848	26	20	1	No	No	7, 42
44	Q96PM5	RCHY1	0.136242	42	22	1	No	No
45	Q92754	TFAP2C	0.135754	86	98	1	No	No
46	Q9Y478	PRKAB1	0.134543	98	96	0	No	No
47	O14920	IKBKB	0.132882	62	53	0	No	Yes	12, 15, 19, 45
48	P21980	TGM2	0.132793	60	81	0	No	No	1
49	Q9Y572	RIPK3	0.13256	92	75	0	No	No
50	P42858	HTT	0.131761	4	10	0	No	No	21

The first column provides the Uniprot id of the gene, the second column provides the gene name. The third column provides the weight of each gene based on M _bw. The fourth and the fifth columns provide the number of instances each gene is expressed in the normal and tumor samples respectively. The sixth column provides the number of mutations of a gene observed throughout all the tumor samples in the dataset. The seventh column indicates whether the gene is listed in the breast cancer pathway of the first golden standard, the NCBI BioSystems, whereas the eight columnd indicates whether it is listed in the second golden standard, the COSMIC database. The last column provides the set of PPI network neighbors of the corresponding gene from the top 50 list that are also in MWIS

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ISSN: 1752-0509

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