Loading…

CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting

All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. We describe here a program pipeline aimed at identifying t...

Full description

Saved in:
Bibliographic Details
Published in:BMC bioinformatics 2004-03, Vol.5 (1), p.27-27, Article 27
Main Authors: Bigelow, Henry R, Wenick, Adam S, Wong, Allan, Hobert, Oliver
Format: Article
Language:English
Subjects:
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription factor targets.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-5-27