This website allows you to browse known and discovered motifs for the ENCODE TF ChIP-seq datasets.

Citation: Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

Pouya Kheradpour and Manolis Kellis
Nucleic Acids Research, 2013 December 13, doi:10.1093/nar/gkt1249

Send any questions/comments to Pouya Kheradpour.

  1. Each experiment is put into a "factor group" on the basis of ChIP TF and its known motifs with the intention to group factors with very similar motifs. Known motifs are assigned to the factor group using the same critera.
  2. The navigation is done in the left frame. For each factor group it indicates the the number of known motifs, discovered motifs, and experimental datasets. Clicking on the headers will resort the table.
  3. The "discovered motifs" for each factor group are the top 10 (in terms of enrichment in their discovery dataset using the Intergenic background) where no two are more than 0.75 similar to each other (this prevents very similar variants of the same motif from being taken).
  4. Enrichments are computed by taking the fraction of motif instances that are inside the bound regions and dividing that by the fraction of shuffle motif instances inside (where the bound regions are filtered against the background regions, defined below). They are also corrected for small counts by using a confidence interval (with Z=1.5) around each fraction and taking the extreme which leads to the enrichment closest to 1.
  5. Clicking on a factor group will change the middle and right frames.
  6. Motifs are matched to the genome using a p-value of 4^-8 (threshold for each motif computed using TFM-PVALUE). A custom program is used to do the actual matching.
  7. motif-disc.pdf (13M): A printable version of the web page with logos and heatmaps for each factor group.
  8. encode-motifs-v1.2.tar.gz (43K): software to (1) compute enrichments and produce heatmaps on custom data and (2) perform unified motif discovery. See README contained within for more information.
  9. The following bulk datafiles are available:

Last modified on 2014-03-14.

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