Evaluating tools for transcription factor binding site prediction

BMC Bioinformatics

Table 3 Normalised Euclidean distances between PWMs derived using the different motif discovery tools and PWMs derived from ChIP-Seq, SELEX or individual promoter assays obtained from JASPAR

	JASPAR.2010	JASPAR.2014	rGADEM	HOMER	ChIPMunk	MEME-ChIP
JASPAR.2010	0	—	—	—	—	—
JASPAR.2014	0.393	0	—	—	—	—
rGADEM	0.660	0.404	0	—	—	—
HOMER	0.503	0.234	0.159	0	—	—
ChIPMunk	0.471	0.192	0.263	0.120	0	—
MEME-ChIP	0.404	0.129	0.371	0.203	0.153	0

Note that comparisons between the matrices generated in this work were performed over the 12 TFBS PWMs that were used for performance evaluation (i.e. the PAZAR-E dataset) while the comparisons with JASPAR.2010 and JASPAR.2014 were performed over the 11 PWMs for which binding sites are found in PAZAR and the ENCODE-ChIP-Seq data and which also have PWMs in JASPAR (i.e. the intersection of the PAZAR-E and PAZAR-J datasets)

ISSN: 1471-2105