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

BMC Bioinformatics. 2004 Mar 12;5:27. doi: 10.1186/1471-2105-5-27.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Caenorhabditis / genetics*
  • Caenorhabditis elegans / genetics*
  • Computational Biology / methods
  • DNA Footprinting / methods*
  • DNA, Helminth / genetics
  • DNA, Intergenic / genetics
  • Databases, Genetic
  • Genes, Helminth / genetics*
  • Genome*
  • Internet
  • Phylogeny*
  • Sequence Homology, Nucleic Acid
  • Software Design
  • Software Validation
  • Software*
  • Transcription Factors / genetics*


  • DNA, Helminth
  • DNA, Intergenic
  • Transcription Factors