Whole-Genome rVISTA | Datasets2Tools

General Information

Description	A tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data
Homepage	http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl

Publications

Bioinformatics (2013)

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

Inna Dubchak; Matthew Munoz; Alexandre Poliakov; Nathan Salomonis; Simon Minovitsky; Rolf Bodmer; Alexander C. Zambon

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.

Contact: azambon@ucsd.edu or ildubchak@lbl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btt318

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