Identifying driver genes involving gene dysregulated expression, tissue-specific expression and gene-gene network

BMC Medical Genomics

Table 3 Co-citer analysis of top 30 breast cancer driver genes identified by our method

Genes	Cancer	Breast	Driver	is driver	DyTidriver	Diffusion	DriverNet	DawnRank	Muf max	Muf sum
TP53	6772	1356	110	1	1	233	1	2	7	2
PIK3CA	1199	334	54	1	2	156	2	1	2	3
MAP 3 K1	135	62	2	1	3	128	18	4	899	28
GATA3	154	122	8	1	4	85	13	6	888	17
CDH1	1410	358	19	1	5	42	4	10	1	6
ERBB2	5335	4332	78	1	6	72	64	90	8	73
UBC	134	30	2	0	7	240	3	122	22	1
NCOR1	109	45	3	1	8	139	12	48	6	68
ASH1L	4	0	1	0	9	1097	NA	1986	1846	729
PIK3R1	131	21	7	1	10	160	10	26	13	45
EP300	269	86	4	1	11	68	5	178	367	4
DYNC1H1	9	2	2	0	12	63	8	17	1017	107
HUWE1	29	4	3	0	13	251	28	45	9	112
PTEN	3047	672	64	1	14	185	98	193	3	79
MAP 3 K13	2	0	1	1	15	6189	NA	3303	2654	2045
NF1	165	24	11	1	16	141	41	19	4	144
TTN	10	1	2	0	17	2581	6	5	717	5
TPP2	4	0	2	0	18	1041	NA	2674	3172	2926
UFL1	7	1	1	0	19	802	NA	NA	3493	3129
BRCA1	4652	4017	22	1	20	25	11	NA	361	27
BACH2	8	1	2	0	21	810	1182	2366	2298	1079
JAK2	382	92	19	1	22	118	32	NA	73	119
ERBB3	354	178	4	1	23	73	29	8	10	207
ERBB4	350	220	4	1	24	74	56	276	18	410
MAP 2 K4	70	10	2	1	25	127	34	23	898	86
CTCF	63	21	3	1	26	55	20	211	1027	29
PRKCB	41	9	1	1	27	174	59	31	80	151
SASH1	13	8	1	0	28	1011	NA	NA	3706	4179
TAF1	10	3	1	1	29	225	86	33	359	19
SPTA1	3	0	1	0	30	212	17	25	1018	109

The second to the fourth column show the co-appeared times of top 30 identified genes with ‘driver’, ‘breast’ and ‘cancer’ (from the left to the right). is_driver indicates whether the given gene is a driver or not in the benchmark dataset. The left columns represent the ranking positions of identified genes in Dytidriver, Diffusion, DriverNet, DawnRank, Muf_max, Muf_sum respectively

ISSN: 1755-8794