title: Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.
abstract: BACKGROUND
  Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.
  
  
  RESULTS
  We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.
  
  
  CONCLUSIONS
  Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. hchiba@hgc.jp <hchiba@hgc.jp>
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Chiba
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D005796:Genes / Q000235:genetics*; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D017385:Sequence Homology; D013045:Species Specificity