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CoGemiR: a comparative genomics microRNA database

Maselli, V; Di Bernardo, D; Banfi, S; (2008) CoGemiR: a comparative genomics microRNA database. BMC Genomics , 9 , Article 457. 10.1186/1471-2164-9-457. Green open access

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Abstract

BACKGROUND: MicroRNAs are small highly conserved non-coding RNAs which play an important role in regulating gene expression by binding the 3'UTR of target mRNAs. The majority of microRNAs are localized within other transcriptional units (host genes) and are co-expressed with them, which strongly suggests that microRNAs and corresponding host genes use the same promoter and other expression control elements. The remaining fraction of microRNAs is intergenic and is endowed with an independent regulatory region. A number of databases have already been developed to collect information about microRNAs but none of them allow an easy exploration of microRNA genomic organization across evolution. RESULTS: CoGemiR is a publicly available microRNA-centered database whose aim is to offer an overview of the genomic organization of microRNAs and of its extent of conservation during evolution in different metazoan species. The database collects information on genomic location, conservation and expression data of both known and newly predicted microRNAs and displays the data by privileging a comparative point of view. The database also includes a microRNA prediction pipeline to annotate microRNAs in recently sequenced genomes. This information is easily accessible via web through a user-friendly query page. The CoGemiR database is available at http://cogemir.tigem.it/ CONCLUSION: The knowledge of the genomic organization of microRNAs can provide useful information to understand their biology. In order to have a comparative genomics overview of microRNAs genomic organization, we developed CoGemiR. To achieve this goal, we both collected and integrated data from pre-existing databases and generated new ones, such as the identification in several species of a number of previously unannotated microRNAs. For a more effective use of this data, we developed a user-friendly web interface that simply shows how a microRNA genomic context is related in different species.

Type: Article
Title: CoGemiR: a comparative genomics microRNA database
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2164-9-457
Publisher version: http://dx.doi.org/10.1186/1471-2164-9-457
Language: English
Additional information: © 2008 Maselli et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Maselli, Vincenza Di Bernardo, Diego Banfi, Sandro Research Support, Non-U.S. Gov't England BMC genomics BMC Genomics. 2008 Oct 6;9:457
Keywords: Animals, Computational Biology, Database Management Systems, Databases, Nucleic Acid, Genomics, MicroRNAs, Genetics, Sequence Analysis, RNA, User-Computer Interface
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/1307453
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