{"url": "http://motifmap.ics.uci.edu/#GeneSearch", "content": "\r\n\r\n \r\n \r\n Motifmap \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n

MotifMap: genome-wide maps of regulatory elements.

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

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Getting Started

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

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

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

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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.

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New! MotifMap-RNA Portal

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\nA 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\ndatabases with querying functions similar to the Motif Search and Gene Search functions on this site (some results are unpublished).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\nit in addition to MotifMap. Now includes access to hg38 MotifMap results under the MotifMap section (for testing only).\n
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BBLS Code

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\n\t\t\t Documented Python code for computing the Bayesian\nBranch Length Score is available here. The code and\nMotifMap data are freely available for academic use. For commercial\nlicenses, please contact: igb-license [at] ics [.] uci [.] edu.\n
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Available Species

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SpeciesHumanHumanMouseFlyYeastWorm
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Buildhg18hg19mm9dm3sacCer2ce6
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Alignmentmultiz28way placentalmultiz46way placentalmultiz30waymultiz15way flies-onlymultiz7waymultiz6way
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Download data

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Species\n\t\t\t\t\t\t\t\t\tHuman\n\t\t\t\t\t\t\t\t\tMouse\n\t\t\t\t\t\t\t\t
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Build\n\t\t\t\t\t\t\t\t\thg19\n\t\t\t\t\t\t\t\t\tmm9\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t
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Alignment\n\t\t\t\t\t\t\t\t\tmultiz46way\n\t\t\t\t\t\t\t\t\tmultiz30way\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t
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Citing MotifMap

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

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

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Acknowledgement

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

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Select species track and click next

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Select motif and click next

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

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Set filters and click search to list binding sites

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Filters

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cid Location +/- BBLS BLS NLOD Z-Score FDR Closest Gene Distance (bp) Description
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Select species (alignment) and click next

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

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Set filters and click search to list binding sites

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Filters:

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cid Location +/- BBLS BLS NLOD Z-Score FDR Motif ID TF Name Gene Distance (bp) Region
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Motif ID Name BBLS BLS NLOD ZScore FDR Distance (bp) Species
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Select species (alignment) and click next

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Select genome location and click search

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\r\n Chromosome\r\n \r\n
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\r\n Location\r\n \r\n
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\r\n Region Length\r\n \r\n
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Filters:

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cid Location Strand BBLS BLS NLOD Z-Score FDR Motif ID TF Name
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M o t i f M a p :: Copyright © University of California, Irvine :: ICS :: IGB
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