is a Data Source.
MotifMap is a system from UC Irvine that provides integrative genome-wide maps of predicted transcription factor binding sites (regulatory motifs) across the human genome and other model species. It combines databases of transcription factor binding motifs, refined multiple-genome alignments, and a comparative genomic statistical scoring approach (Bayesian Branch Length Score) to call candidate regulatory motif sites with associated false discovery rates. The released maps cover yeast, fly, worm, mouse, and human, with the human map containing over 500,000 sites for hundreds of motif matrices. MotifMap is an upstream source of the GenomicKB knowledge graph.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| motifmap.portal | MotifMap Web Portal | motifmap.ics.uci.edu | GraphicalInterface | ❔ | Historical MotifMap web portal at UC ... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| genomickb.graph | GenomicKB Graph Dump | genomickb-a-knowledgebase-for-the-human-genome | GraphProduct | http | had primary source | GenomicKB 1.0 Neo4j Database Dump (Re... |
MotifMap, developed at the University of California, Irvine, provides integrative genome-wide maps of candidate regulatory motif sites, focusing on predicted transcription factor binding sites across the human genome and other model species. The system combines curated transcription factor binding motif databases with refined multiple-genome alignments and a comparative genomic statistical approach to score and report candidate sites along with false discovery rate estimates.
The published maps span yeast, fly, worm, mouse, and human, and were designed to be integrated with other omics data to support genome-wide analysis of gene regulation. MotifMap serves as an upstream source of the GenomicKB knowledge graph.
The original MotifMap web service is no longer reachable: the canonical homepage
subdomain (motifmap.ics.uci.edu, formerly also motifmap.igb.uci.edu) does
not resolve in DNS, and the sibling MotifMap-RNA service returns a server error.
The resource is recorded here as inactive, with the live BMC Bioinformatics
article used as the stable reference homepage.
Created: June 18, 2026 | Last modified: June 18, 2026