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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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Related in: MedlinePlus

The Result page. The CoGemiR Results table summarizes the main information about the queried microRNAs. Panels A and B show the results obtained after querying the database, respectively, with the tems "miR-25" and "mir-585" in all species (more details are provided in the text). Please note that the gene GSTENG00029242001 listed in panel A is the tetraodon homolog of the Mcm7 gene, as assessed by EnsEMBL analysis.
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Figure 4: The Result page. The CoGemiR Results table summarizes the main information about the queried microRNAs. Panels A and B show the results obtained after querying the database, respectively, with the tems "miR-25" and "mir-585" in all species (more details are provided in the text). Please note that the gene GSTENG00029242001 listed in panel A is the tetraodon homolog of the Mcm7 gene, as assessed by EnsEMBL analysis.

Mentions: The "Results" page contains a summary of the main information about the queried microRNAs (Figure 4). The user can choose the columns to be visualized. The first column ("MicroRNA") reports the name of the microRNA linked to the "extra feature" page (see below), the "conservation" column, which only appears when a single species is selected in the query, provides a link to the list of species in which the microRNA is present, the "family" column provide a link to the list of the microRNAs belonging to the same family in all species, the "miRBase" column provides a direct link to miRBase whereas the "genomic coordinates" column and the "overlapping gene" column, which contain the name of the gene overlapping the microRNA, provide links to EnsEMBL (release 48). The last three columns indicate the microRNA localization, the rank of the intron/exon of the gene in which intragenic microRNAs are embedded and the status of the microRNA, i.e., annotated or predicted. For the CoGemiR predicted microRNAs, the "status" column provides a link to the secondary structure prediction data. As shown in Figure 3, the "Results" page allows to obtain an evolutionary overview of microRNA genomic features. For example, it is possible to simultaneously assess the genomic localization of a given microRNA in all the analyzed species, as shown in Figure 4.


CoGemiR: a comparative genomics microRNA database.

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

The Result page. The CoGemiR Results table summarizes the main information about the queried microRNAs. Panels A and B show the results obtained after querying the database, respectively, with the tems "miR-25" and "mir-585" in all species (more details are provided in the text). Please note that the gene GSTENG00029242001 listed in panel A is the tetraodon homolog of the Mcm7 gene, as assessed by EnsEMBL analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: The Result page. The CoGemiR Results table summarizes the main information about the queried microRNAs. Panels A and B show the results obtained after querying the database, respectively, with the tems "miR-25" and "mir-585" in all species (more details are provided in the text). Please note that the gene GSTENG00029242001 listed in panel A is the tetraodon homolog of the Mcm7 gene, as assessed by EnsEMBL analysis.
Mentions: The "Results" page contains a summary of the main information about the queried microRNAs (Figure 4). The user can choose the columns to be visualized. The first column ("MicroRNA") reports the name of the microRNA linked to the "extra feature" page (see below), the "conservation" column, which only appears when a single species is selected in the query, provides a link to the list of species in which the microRNA is present, the "family" column provide a link to the list of the microRNAs belonging to the same family in all species, the "miRBase" column provides a direct link to miRBase whereas the "genomic coordinates" column and the "overlapping gene" column, which contain the name of the gene overlapping the microRNA, provide links to EnsEMBL (release 48). The last three columns indicate the microRNA localization, the rank of the intron/exon of the gene in which intragenic microRNAs are embedded and the status of the microRNA, i.e., annotated or predicted. For the CoGemiR predicted microRNAs, the "status" column provides a link to the secondary structure prediction data. As shown in Figure 3, the "Results" page allows to obtain an evolutionary overview of microRNA genomic features. For example, it is possible to simultaneously assess the genomic localization of a given microRNA in all the analyzed species, as shown in Figure 4.

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
Related in: MedlinePlus