title: Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl.
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ildubchak@lbl.gov
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: Matthew
authors.initials: M
authors.lastname: Munoz
authors.forename: Alexandre
authors.initials: A
authors.lastname: Poliakov
authors.forename: Nathan
authors.initials: N
authors.lastname: Salomonis
authors.forename: Simon
authors.initials: S
authors.lastname: Minovitsky
authors.forename: Rolf
authors.initials: R
authors.lastname: Bodmer
authors.forename: Alexander C
authors.initials: AC
authors.lastname: Zambon
mesh_terms: D000465:Algorithms; D000818:Animals; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors