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Bioinformatics. 2013 Aug 15;29(16):2059-61. doi: 10.1093/bioinformatics/btt318. Epub 2013 Jun 4.

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.

Author information

1
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ildubchak@lbl.gov

Abstract

SUMMARY:

We have developed a web-based query tool, Whole-Genome rVISTA (WGRV), that determines enrichment of transcription factors (TFs) and associated target genes in sets of co-regulated genes. WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp to 5 kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position-weight matrices from the TRANSFAC Professional database. For a given set of co-regulated genes, WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the regulatory VISTA (rVISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters. Results are exported in a BED format for rapid visualization in the UCSC genome browser. Flat files of mapped conserved sites and their genomic coordinates are also available for analysis with stand-alone software.

AVAILABILITY:

http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl.

PMID:
23736530
PMCID:
PMC3722517
DOI:
10.1093/bioinformatics/btt318
[Indexed for MEDLINE]
Free PMC Article
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