Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines

BMC Systems Biology

Table 3 Enrichment of driver/regulator binding motifs on passenger promoters of mRNA association modules

index	reg	N ₁	N ₂	N ₃	p-value
44	MITF	118	2023	23	0.0464
45	TBP	77	8009	56	5.3704 × 10^-4
45	MYB	77	10684	65	0.0076
46	SREBF2	49	9755	36	0.1581
47	E2F3	31	8123	21	0.0989
47	NFYA	31	2170	3	0.8513
47	SRF	31	75	0	1.0
51	NFATC3	22	2170	5	0.2097
53	NFKB2	19	531	0	1.0
66	TP53	35	3576	16	0.0041
76	PAX8	61	5376	34	0.0014
78	HOXC13	19	5421	12	0.0164
79	PPARG	13	20	0	1.0
81	mir-96	121	636	11	0.0147
81	mir-106a	121	319	6	0.0463
81	mir-17	121	830	12	0.0379
81	mir-93	121	832	12	0.0385
81	mir-106	121	718	11	0.0323
82	mir-21	120	291	7	0.0093
83	SMAD3	338	10025	271	1.058 × 10^-7
84	ERG	338	2231	67	0.0093
84	ELK4	338	2803	76	0.0518
84	NFATC1	338	10187	265	3.1517 × 10^-5
84	RFX3	338	2751	75	0.0481
84	POU5F	338	379	18	0.0027

Index: module index. Reg: the transcription factor or microRNA with putative targets. N₁: number of passenger genes in a module. N₂: total number of putative targets in human genes. N₃: number of passenger genes containing the transcription factor binding motif. p-value: hyper-geometric p-value of enrichment. For modules with microRNAs as drivers, N₂: number of putative targets of a microRNA. N₃: number of passenger genes belonging to the putative targets of the microRNA.

ISSN: 1752-0509