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

BMC Genomics

Table 2 Top 15 transcription factors enriched in MDA-MB-231 cells

TF name	Motif	Selection by:	TF binding sites	Ref. sites	Expected sites in ref.	Ratio of enrichment	Mean read count
MYBL2	MYBB_f1	2, 3, 4	12	2930	6.2	1.92	2197
BACH1	BACH1_si	1, 2, 3	15	3904	8.3	1.81	531
MYC	MYC_f1	1, 2, 4	10	2698	5.7	1.74	3044
MAFK	MAFK_si	2, 3	16	4428	9.4	1.70	688
RELA	TF65_f2	1, 2, 4	19	5467	11.6	1.63	1398
PPARA	PPARA_f1	1, 2, 3	9	2747	5.8	1.54	185
NFIA/B/C/X	^a	1, 2, 3	15	4669	9.9	1.51	^b
NFIL3	NFIL3_si	1, 2, 3	11	3494	7.4	1.48	474
FOXA2	FOXA2_f1	1, 2, 3	36	11477	24.4	1.47	434
REL	REL_do	1, 2, 3	17	5422	11.5	1.47	69
ZFHX3	ZFHX3_f1	2, 3	46	14683	31.2	1.47	66
RXRB	RXRB_f1	1, 2, 4	20	6414	13.6	1.47	1015
SMARCC1	SMRC1_f1	1, 4	20	6443	13.7	1.46	1478
ETV5	ETV5_f1	2, 3	16	5199	11.1	1.45	641
NR3C1	GCR_si	1, 2, 4	15	4910	10.4	1.44	1087

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. ^aNFIA + NFIB + NFIC + NFIX_f2, ^bRead count range (51, 148, 748, 444, respectively). Ref. reference

ISSN: 1471-2164