Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

BMC Genomics

Table 3 Top 15 transcription factors enriched in T-47D cells

TF name	Motif	Selection by:	TF binding sites	Ref. sites	Expected sites in ref.	Ratio of enrichment	Mean read count
MBD2	MBD2_si	1, 2, 3, 4	101	6664	39.6	2.55	571
TFAP2A	AP2A_f2	1, 2, 3	115	10363	61.6	1.87	941
E4F1	E4F1_f1	2, 3	18	1750	10.4	1.73	310
SP1	SP1_f1	1, 2	392	41453	246.3	1.59	838
CUX1	CUX1_f1	1, 2, 3	13	1462	8.7	1.50	141
E2F2	E2F2_f1	1, 2	17	1941	11.5	1.47	215
AHR	AHR_si	1, 2, 3	9	1030	6.1	1.47	791
SP2	SP2_si	1, 2	140	16512	98.1	1.43	672
CREB1	CREB1_f1	1, 2, 3	23	2720	16.2	1.42	177
CBFB	PEBB_f1	1, 2, 3, 4	46	5461	32.4	1.42	457
ZIC2	ZIC2_f1	1, 2, 3	46	5487	32.6	1.41	118
ZFX	ZFX_f1	1, 2, 3	127	15650	93.0	1.37	287
HIF1A	HIF1A_si	1, 2, 3, 4	15	1890	11.2	1.34	1847
E2F3	E2F3_si	1, 2, 3	16	2019	12.0	1.33	322
XBP1	XBP1_f1	1, 3, 4	12	1545	9.2	1.31	22744

The ratio of enrichment is the result of dividing the number of TF binding sites by the number of expected sites. Motifs are derived from the HOCOMOCO database. Ref. reference

ISSN: 1471-2164