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dc.contributor.authorFukuoka, Yutaka
dc.contributor.authorInaoka, Hidenori
dc.contributor.authorKohane, Isaac Samuel
dc.date.accessioned2012-05-01T18:58:11Z
dc.date.issued2004
dc.identifier.citationFukuoka, Yutaka, Hidenori Inaoka, and Isaac S Kohane. 2004. Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics 5: 4.en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:8646725
dc.description.abstractBackground: 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 duplic ated genes. Conclusion: 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.en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi://10.1186/1471-2164-5-4en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC331401/pdf/en_US
dash.licenseLAA
dc.subjectco-expressionen_US
dc.subjectinter-species comparisonen_US
dc.subjecthromosomal distanceen_US
dc.subjecteukaryotic genomeen_US
dc.titleInter-Species Differences of Co-expression of Neighboring Genes in Eukaryotic Genomesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalBMC Genomicsen_US
dash.depositing.authorKohane, Isaac Samuel
dc.date.available2012-05-01T18:58:11Z
dash.affiliation.otherHMS^Countway Library of Medicineen_US
dash.affiliation.otherHMS^Medicine-Brigham and Women's Hospitalen_US
dash.affiliation.otherHMS^Pediatrics-Children's Hospitalen_US
dc.identifier.doi10.1186/1471-2164-5-4*
dash.contributor.affiliatedKohane, Isaac


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