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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

From: Evaluating tools for transcription factor binding site prediction

  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
  1. 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)