MotifMap: genome-wide maps of regulatory elements.

Motif Search allows users to select a transcription factor, view its binding sequence logo, and list its genome-wide putative binding sites.

Gene Search allows users to select a gene and search for transcription factor binding sites in regions upstream and downstream from its transcription start site.

SNPer allows users to select a genomic loci (e.g. a SNP) and search for overlapping or neighbouring transcription factor binding sites.

In all cases, users can filter the results by various criteria and export them to severals file formats or view them directly in the UCSC genome browser.

A new portal for all MotifMap functions including the new MotifMap-RNA functions is available at MotifMap-RNA web portal. It includes MotifMap-RNA, MotifMap with new genome builds and ChIPSeq databases with querying functions similar to the Motif Search and Gene Search functions on this site (some results are unpublished). If you use MotifMap-RNA, please cite it in addition to MotifMap. Now includes access to hg38 MotifMap results under the MotifMap section (for testing only).

Documented Python code for computing the Bayesian Branch Length Score is available here. The code and MotifMap data are freely available for academic use. For commercial licenses, please contact: igb-license [at] ics [.] uci [.] edu.

Kenneth Daily, Vishal R Patel, Paul Rigor, Xiaohui Xie, and Pierre Baldi. "MotifMap: integrative genome-wide maps of regulatory motif sites for model species" BMC Bioinformatics 2011, 12:495 (doi:10.1186/1471-2105-12-495)

Xiaohui Xie, Paul Rigor, and Pierre Baldi. "MotifMap: a human genome-wide map of candidate regulatory motif sites." Bioinformatics 2009; 25: 167 - 174. (doi:10.1093/bioinformatics/btn605)