Differential motif enrichment analysis of paired ChIP-seq experiments

BMC Genomics

Table 5 Local motif enrichment in bound and unbound promoters in untreated MCF10A-ER-Src cells

	FOS		MYC		STAT3
	Motif	Rank	Motif	Rank	Motif	Rank
Local Enrichment: Proximal TSSs	SP4_full	1	SP4_full	1	KLF14_DBD	1
	Fos	288	Mycn	365	STAT1	125
	Mycn	323	STAT1	482	Mycn	505
	STAT1	874	Fos	587	Fos	541
Differential Enrichment: Proximal vs. Distal TSSs	JDP2_DBD	1	NFYA	1	Stat3	1
	Fos	11	Myc	63	MYC::MAX	795
	Mycn	33	Fos	532	Fos	829
	STAT1	857	STAT1	559

The table summarizes local motif enrichment around TSSs proximal (within 1000 bp) or distal to the nearest peak in FOS, MYC and STAT3 ChIP-seq experiments in untreated MCF10A-ER-Src cells. For each ChIP-ed factor, we report the name (in the JASPAR+Jolma compendium) and rank (out of 884) of the most significantly enriched motif from each of the three ChIP-ed TF families. in untreated MCF10A-ER-Src cells. Rank is based on either the local enrichment in bound promoters (“Proximal TSSs”) or the differential local enrichment between bound and unbound promoters (“Proximal vs. Distal TSSs”). The top-ranking motif is also shown even if it is not from on of the three ChIP-ed TF families. The numbers of proximal (distal) TSSs are FOS: 4503 (44548); MYC: 11192 (37859); and STAT3: 2261 (46790).

ISSN: 1471-2164