title: Inter-species differences of co-expression of neighboring genes in eukaryotic genomes.
abstract: BACKGROUND
  There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human.
  
  
  RESULTS
  We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8-30 % of the highly co-expressed pairs are duplicated genes.
  
  
  CONCLUSIONS
  We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
authors.affiliation: Department of Biosystem Modeling, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan. fukuoka.bmi@tmd.ac.jp
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Fukuoka
authors.forename: Hidenori
authors.initials: H
authors.lastname: Inaoka
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics; D005057:Eukaryotic Cells / Q000378:metabolism*; D015870:Gene Expression / Q000235:genetics*; D023061:Gene Order; D016678:Genome; D006801:Humans; D051379:Mice; D011506:Proteins / Q000235:genetics; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D011506:Proteins