Additional file 5: Figure S3.

Sequence logos for VDR-like binding site motifs. The motifs were identified for each data set by searching the full ChIP-Seq regions with the Jaspar/TRANSFAC RXRA::VDR motif using MAST, followed by de novo motif discovery with MEME on the positive regions from MAST [15]. The resulting VDR-like matrix was used for another round of MAST searching on the full ChIP-Seq regions and MEME motif discovery on the positive set. The final matrices are shown for (A) LCL (434 sites used by MEME), (B) MCL (288 sites), (C) CD4+ (56 sites), and (D) Jaspar/TRANSFAC RXRA::VDR. The observation that the LCL and MCL logos are more similar to each other than to the RXRA::VDR logo, whereas the logo for CD4+ is more similar to the RXRA::VDR logo, may reflect the fact that the two first logos are based on a much larger number of sites and are, therefore, more likely to represent the true binding site motif for strong binding.

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Handel et al. BMC Medicine 2013 11:163   doi:10.1186/1741-7015-11-163