Inter-Species Differences of Co-expression of Neighboring Genes in Eukaryotic Genomes

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Inter-Species Differences of Co-expression of Neighboring Genes in Eukaryotic Genomes

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Title: Inter-Species Differences of Co-expression of Neighboring Genes in Eukaryotic Genomes
Author: Fukuoka, Yutaka; Inaoka, Hidenori; Kohane, Isaac Samuel

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Citation: Fukuoka, Yutaka, Hidenori Inaoka, and Isaac S Kohane. 2004. Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics 5: 4.
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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 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.
Published Version: doi://10.1186/1471-2164-5-4
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC331401/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8646725
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