Locational distribution of gene functional classes in Arabidopsis thaliana

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dc.contributor.author Riley, Michael Charles
dc.contributor.author Clare, Amanda
dc.contributor.author King, Ross Donald
dc.date.accessioned 2008-08-19T07:56:37Z
dc.date.available 2008-08-19T07:56:37Z
dc.date.issued 2007-03-30
dc.identifier.citation Riley , M C , Clare , A & King , R D 2007 , ' Locational distribution of gene functional classes in Arabidopsis thaliana ' BMC Bioinformatics , vol 8 , 112 . , 10.1186/1471-2105-8-112 en
dc.identifier.issn 1471-2105
dc.identifier.other PURE: 77378
dc.identifier.other dspace: 2160/634
dc.identifier.uri http://hdl.handle.net/2160/634
dc.identifier.uri http://www.biomedcentral.com/1471-2105/8/112 en
dc.description Riley, M. C., Clare, A., King, R. D. (2007). Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics 8, Article No: 112 Sponsorship: EPSRC / RAEng en
dc.description.abstract Background: We are interested in understanding the locational distribution of genes and their functions in genomes, as this distribution has both functional and evolutionary significance. Gene locational distribution is known to be affected by various evolutionary processes, with tandem duplication thought to be the main process producing clustering of homologous sequences. Recent research has found clustering of protein structural families in the human genome, even when genes identified as tandem duplicates have been removed from the data. However, this previous research was hindered as they were unable to analyse small sample sizes. This is a challenge for bioinformatics as more specific functional classes have fewer examples and conventional statistical analyses of these small data sets often produces unsatisfactory results. Results: We have developed a novel bioinformatics method based on Monte Carlo methods and Greenwood's spacing statistic for the computational analysis of the distribution of individual functional classes of genes (from GO). We used this to make the first comprehensive statistical analysis of the relationship between gene functional class and location on a genome. Analysis of the distribution of all genes except tandem duplicates on the five chromosomes of A. thaliana reveals that the distribution on chromosomes I, II, IV and V is clustered at P = 0.001. Many functional classes are clustered, with the degree of clustering within an individual class generally consistent across all five chromosomes. A novel and surprising result was that the locational distribution of some functional classes were significantly more evenly spaced than would be expected by chance. Conclusion: Analysis of the A. thaliana genome reveals evidence of unexplained order in the locational distribution of genes. The same general analysis method can be applied to any genome, and indeed any sequential data involving classes. en
dc.language.iso eng
dc.relation.ispartof BMC Bioinformatics en
dc.title Locational distribution of gene functional classes in Arabidopsis thaliana en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-8-112
dc.contributor.institution Department of Computer Science en
dc.contributor.institution Bioinformatics and Computational Biology Group en
dc.description.status Peer reviewed en


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