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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/33366

Title: CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands
Authors: Barturen, Guillermo
Geisen, Stefanie
Dios, Francisco
Maarten Hamberg, E. J.
Hackenberg, Michael
Oliver, José Luis
Issue Date: 2013
Abstract: Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.
Sponsorship: This work was supported by the Spanish Government [BIO2008-01353 to José L. Oliver and BIO2010-20219 to Michael Hackenberg], Basque country “AE” grant (to Guillermo Barturen) and Erasmus internships (to Stefanie Geisen, Francisco Dios, and E. J. Maarten Hamberg).
Publisher: Hindawi Publishing Corporation
Keywords: CpGislandEVO
Database
GEnome
URI: http://hdl.handle.net/10481/33366
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Citation: Barturen, G.; et al. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands. Biomed Research International, 2013: 709042 (2013). [http://hdl.handle.net/10481/33366]
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