title: CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting.
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.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032, USA. hrb46@columbia.edu
authors.forename: Henry R
authors.initials: HR
authors.lastname: Bigelow
authors.forename: Adam S
authors.initials: AS
authors.lastname: Wenick
authors.forename: Allan
authors.initials: A
authors.lastname: Wong
authors.forename: Oliver
authors.initials: O
authors.lastname: Hobert
mesh_terms: D000818:Animals; D002107:Caenorhabditis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D018983:DNA Footprinting / Q000379:methods*; D018509:DNA, Helminth / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D030541:Databases, Genetic; D017238:Genes, Helminth / Q000235:genetics*; D016678:Genome; D020407:Internet; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D012985:Software Design; D012986:Software Validation; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D018509:DNA, Helminth; D021901:DNA, Intergenic; D014157:Transcription Factors