CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands
Joint Authors
Barturen, Guillermo
Geisen, Stefanie
Dios, Francisco
Hamberg, E. J. Maarten
Hackenberg, Michael
Oliver, José L.
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-09-25
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Barturen, Guillermo& Geisen, Stefanie& Dios, Francisco& Hamberg, E. J. Maarten& Hackenberg, Michael& Oliver, José L.. 2013. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands. BioMed Research International،Vol. 2013, no. 2013, pp.1-6.
https://search.emarefa.net/detail/BIM-1004927
Modern Language Association (MLA)
Barturen, Guillermo…[et al.]. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands. BioMed Research International No. 2013 (2013), pp.1-6.
https://search.emarefa.net/detail/BIM-1004927
American Medical Association (AMA)
Barturen, Guillermo& Geisen, Stefanie& Dios, Francisco& Hamberg, E. J. Maarten& Hackenberg, Michael& Oliver, José L.. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-6.
https://search.emarefa.net/detail/BIM-1004927
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1004927