A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

BMC Genomics

Table 3 Recent ChIP-seq studies

Transcription Factor(s)	Organism	Algorithm(s)	Negative control sample	qPCR validations	Reference	Time of publication
Scl/Tal1	Mus musculus	FindPeaks	no	>10	[32]	5/2009
ERalpha	Homo sapiens	FindPeaks (MACS)	yes	>10	[33]	5/2009
STAT1	Homo sapiens	PeakSeq	yes	>100	[12]	1/2009
CTCF	Homo sapiens	SISSRs	no	not reported	[34]	1/2009
Cse4, Ste12	Saccharomyces cerevisiae	PeakSeq	yes	<10	[35]	1/2009
PPARg, RXR	Mus musculus	FindPeaks	no	>10	[36]	11/2008
Stat5a, Stat5b	Mus musculus	MACS	yes	<10	[25]	11/2008
NRSF, SRF, GABP	Homo sapiens	QuEST	yes	not reported	[8]	9/2008
FoxA1	Homo sapiens	MACS (PeakFinder, QuEST, FindPeaks)	yes	not reported	[10]	9/2008
NRSF	Homo sapiens	PeakFinder	yes	>100	[2]	6/2007

Representative examples of recent ChIP-seq studies with publicly available datasets were collected from the Gene Expression Omnibus (GEO). Additionally, the public datasets used in the present study were included. The column Algorithm(s) indicates the algorithm applied in the original study. If other algorithms were also considered, they are listed in the brackets. The column qPCR validations indicates the level of experimental validation in terms of the numbers of validated regions.

ISSN: 1471-2164