De novo motif analysis was carried out on the central 100 bps of the peak regions using Homer. For any ChIP-Seq experiment in CODEX, all peak regions were used as input to the
findMotifsGenome.pl script in Homer. The program then looks for consensus sequences that are enriched in the sample relative to background (randomly selected sequences from the genome). The resulting HTML page and the motif position weight matrices (PWM) are displayed on CODEX.
For more information about Homer and results, see:
Although Homer performs searches for known motifs, CODEX also displays results from an independent search conducted on a larger set of known motifs using TOMTOM. Known motifs were collected in-house from publications and public resources (Jaspar, UniProbe and Jolma et al.). PWMs of enriched motifs found by Homer that passed the quality threshold (p-value<=1e-10 and %target >= 5%) were converted to MEME format and used as input to TOMTOM. Significant similarities of enriched motifs to known motifs are reported in a HTML output on CODEX. For more information about TOMTOM, see:
For more information about TOMTOM, see: