cpgislandevo: a database and genome browser for comparative evolutionary genomics of cpg islands

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ID: 131926
2013
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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.
Reference Key
barturen2013biomedcpgislandevo: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Guillermo Barturen;Stefanie Geisen;Francisco Dios;E. J. Maarten Hamberg;Michael Hackenberg;José L. Oliver
Journal spectrochimica acta - part a: molecular and biomolecular spectroscopy
Year 2013
DOI
10.1155/2013/709042
URL
http://dx.doi.org/10.1155/2013/709042
Keywords
Medicine

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