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CoGemiR: a comparative genomics microRNA database.

Maselli V, Di Bernardo D, Banfi S - BMC Genomics (2008)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: TIGEM Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples Italy. maselli@tigem.it

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.

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Search page. In the CoGemiR search page a user-friendly form guides the user in performing the queries.
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Figure 3: Search page. In the CoGemiR search page a user-friendly form guides the user in performing the queries.

Mentions: The main page briefly summarizes CoGemiR aims, provides some statistics and allows the user to submit a quick search (Figure 2). There are tree ways to perform a quick search, i.e., (i) by typing a keyword (e.g., mir-124), (ii) by pasting a list of microRNAs (max 50) or (iii) by uploading a file. The query mask allows the user to perform more complex queries. In the advanced search, all the possible search options are available. In the main search page, the query becomes more and more specific in a step-by-step process, depending on the user's choice. It is possible to retrieve: (1) a specific microRNA in a selected species; (2) the list of microRNAs present in a given species or in a set of species (e.g., all human microRNAs or microRNAs present in all Primates); (3) the list of the species in which a selected microRNA or microRNA family is present. In the latter two cases, the search can also be further restricted by 1) microRNA 'status', i.e., to allow the user to retrieve either predicted or annotated microRNAs only; by 2) 'localization', i.e., to allow retrieval of all the microRNAs with a specific localization (intergenic or intragenic and within the latter category exonic, intronic, etc.); and by 3) expression data, i.e., to allow retrieval of all the microRNAs with an overlapping gene expressed in a specific tissue (option available only for human and mouse). Additional and more complex subqueries are possible by combining status and localization filters (Figure 3). Parts of the form appear only if a filter is selected (e.g., the specific localization filter appear only if intragenic microRNAs are selected). Using wildcards (a question mark immediately after the microRNA name), it is possible to perform less stringent queries, e.g., by entering the query "mir-124?" will yield as results both "mir-124" and "mir-124a" entries.


CoGemiR: a comparative genomics microRNA database.

Maselli V, Di Bernardo D, Banfi S - BMC Genomics (2008)

Search page. In the CoGemiR search page a user-friendly form guides the user in performing the queries.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567348&req=5

Figure 3: Search page. In the CoGemiR search page a user-friendly form guides the user in performing the queries.
Mentions: The main page briefly summarizes CoGemiR aims, provides some statistics and allows the user to submit a quick search (Figure 2). There are tree ways to perform a quick search, i.e., (i) by typing a keyword (e.g., mir-124), (ii) by pasting a list of microRNAs (max 50) or (iii) by uploading a file. The query mask allows the user to perform more complex queries. In the advanced search, all the possible search options are available. In the main search page, the query becomes more and more specific in a step-by-step process, depending on the user's choice. It is possible to retrieve: (1) a specific microRNA in a selected species; (2) the list of microRNAs present in a given species or in a set of species (e.g., all human microRNAs or microRNAs present in all Primates); (3) the list of the species in which a selected microRNA or microRNA family is present. In the latter two cases, the search can also be further restricted by 1) microRNA 'status', i.e., to allow the user to retrieve either predicted or annotated microRNAs only; by 2) 'localization', i.e., to allow retrieval of all the microRNAs with a specific localization (intergenic or intragenic and within the latter category exonic, intronic, etc.); and by 3) expression data, i.e., to allow retrieval of all the microRNAs with an overlapping gene expressed in a specific tissue (option available only for human and mouse). Additional and more complex subqueries are possible by combining status and localization filters (Figure 3). Parts of the form appear only if a filter is selected (e.g., the specific localization filter appear only if intragenic microRNAs are selected). Using wildcards (a question mark immediately after the microRNA name), it is possible to perform less stringent queries, e.g., by entering the query "mir-124?" will yield as results both "mir-124" and "mir-124a" entries.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: TIGEM Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples Italy. maselli@tigem.it

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.

Show MeSH