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

TitleWhole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.
Publication TypeJournal Article
Year of Publication2013
AuthorsDubchak, I, Munoz, M, Poliakov, A, Salomonis, N, Minovitsky, S, Bodmer, R, Zambon, AC
JournalBioinformatics
Volume29
Issue16
Pagination2059-61
Date Published2013 Aug 15
ISSN1367-4811
iDASH CategoryGenomics
AbstractSUMMARY: 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.
DOI10.1093/bioinformatics/btt318
Alternate JournalBioinformatics
PubMed ID23736530