MotifMap: genome-wide maps of regulatory elements.

The MotifMap system provides comprehensive maps of candidate regulatory elements encoded in the genomes of model species using databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach- Bayesian Branch Length Score

Getting Started

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.

BBLS Code

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.

Available Species

SpeciesHumanHumanMouseFlyYeastWorm
Buildhg18hg19mm9dm3sacCer2ce6
Alignmentmultiz28way placentalmultiz46way placentalmultiz30waymultiz15way flies-onlymultiz7waymultiz6way

Download data

Species Human Mouse
Build hg19 mm9

Citing MotifMap

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)

Acknowledgement

Development of motifmap is made possible by funding from the National Science Foundation and the National Institutes of Health.

Select species track and click next

Select motif and click next

Motif ID TF Name Consensus Length
Click on a Motif to view sequence logo

->

Set filters and click search to list binding sites

Filters

BBLS BLS
FDR
NLOD Z-Score
Distance (bp)
cid Location +/- BBLS BLS NLOD Z-Score FDR Closest Gene Distance (bp) Description

Select species (alignment) and click next

Enter a gene name (official gene symbol or refSeq transcript id) and click next

->

Set filters and click search to list binding sites

Filters:

BBLS BLS
FDR
NLOD Z-Score
Upstream Downstream
cid Location +/- BBLS BLS NLOD Z-Score FDR Motif ID TF Name Gene Distance (bp) Region
Motif ID Name BBLS BLS NLOD ZScore FDR Distance (bp) Species

Select species (alignment) and click next

Select genome location and click search

Chromosome
Location
Region Length

Filters:

BBLS BLS
FDR
NLOD Z-Score
cid Location Strand BBLS BLS NLOD Z-Score FDR Motif ID TF Name