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

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 bind

SUBMITTER: Dubchak I 

PROVIDER: S-EPMC3722517 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature