Abstract
BackgroundThere 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.ResultsWe 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.ConclusionWe 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.
Highlights
There is increasing evidence that gene order within the eukaryotic genome is not random
Expression profiles combined with wholegenome information, especially map information, enable us to investigate a relationship between co-expression of genes and a chromosomal distance (CD)
Gene ontology category We investigated Gene Ontology (GO) categories http://www.geneontology.org/ in the highly correlated (HC), negatively correlated (NC) and ZC groups in CD ranges between 0 and 20 kbp and between 980 and 1000 kbp
Summary
There is increasing evidence that gene order within the eukaryotic genome is not random. Adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. In mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. 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. Clustering of coexpressed genes has been found in humans (Homo sapiens) [4], worm [5] and fruit flies (Drosophila melanogaster) [6,7]. We analyzed the effect of distance using 24 expression datasets in six eukaryotic species: yeast, fruit fly, worm, rat (Rattus norvegicus), mouse (Mus musculus) and human and investigated inter-species differences
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
