Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2004 Mar 12;5:27.

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

Author information

  • 1Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032, USA. hrb46@columbia.edu

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

PMID:
15113408
[PubMed - indexed for MEDLINE]
PMCID:
PMC406492
Free PMC Article

Images from this publication.See all images (4)Free text

Figure 1
Figure 2
Figure 3
Figure 4
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Write to the Help Desk