Example: CTCF

We demonstrate the utility of DiffLogo using the motifs of binding sites of the human insulator CTCF in four different cell lines as obtained by motif discovery on preprocessed ChIP-seq data from the ENCODE project. For CTCF motif inference, sequences with p-values smaller than 10-6 were selected. All data are freely available as Additional File of the original publication Eggeling et al., 2014. The used motifs are available as PWM-files and can be downloaded here. Please see also the supported file formats.

We plot the motifs of the cell lines H1-hESC, HeLe-S3, HepG2, and HUVEC. The motifs of HeLe-S3, HepG2, and HUVEC are highly similar, while the motif of H1-hESC is different from these three motifs. Due to leaf ordering, the difference between compared motifs increases with increasing distance from the main diagonal in the difference logo grid.

A more detailed comparison and interpretation of the motifs from the cell lines H1-hESC, MCF7, HeLa-S3, HepG2, and HUVEC can be found in Nettling et al. 2015.