PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

BMC Bioinformatics

Table 1 Characteristics of transcription factor-bound peaks and subpeaks

Factor	Reads mapped	Peaks	Peak length	Subpeaks	Subpeak length	Motifs
			(average/median)		(average/median)	peaks	subpeaks
Ctcf	3446024	46742	398/380	47117	332/319	94/94	95/95
Esrrb	11669746	82552	532/458	122689	315/299	135/166	215/246
Etf1	10245583	27612	1271/946	73888	441/390	-†	-
Klf4	6602662	27381	460/413	33781	301/289	45/55	65/68
c-Myc	10586180	8535	466/406	13115	263/249	0/18	12/27
n-Myc	7563562	15824	498/432	22688	284/269	0/32	16/46
Nanog	3201091	11334	412/385	10905	339/320	0/23	6/22
Oct4	7910224	9818	407/380	10928	293/289	8/20	20/22
Smad1	2530783	989	483/439	907	382/369	0/2	1/2
Sox2	8122529	9611	400/379	10159	316/309	14/20	21/21
Stat3	8533107	7069	326/293	7364	251/239	0/15	10/15
Suz12	8327215	5079	1550/1178	17043	430/389	-‡	-
Tcfcp2l1	10962390	46278	436/399	54856	324/310	2/93	102/110
Zfx	7323252	34348	486/406	49069	244/229	0/69	65/99

^† Alternate motif identified.
^‡ No consensus found.
Summary of ChIP-seq regions occupied by each transcription factor profiled, the numbers of peaks/subpeaks partitioned by PeakSplitter, and the datasets where previously reported binding motifs could be identified. The number of motifs present in transcription factor-bound peak and subpeak datasets are given in the last two columns, indicating improved motif detection from subpeak summit regions.

ISSN: 1471-2105