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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

MicroRNAs distribution across analyzed species. The chart reports the distribution of microRNAs in different species. On the Y-axis the absolute number of microRNAs is reported, on the X-axis the name of the species. In yellow the CoGemiR high confidence (HC) prediction, in red the EnsEMBL prediction and in blue the microRNA present in miRBase.
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Figure 1: MicroRNAs distribution across analyzed species. The chart reports the distribution of microRNAs in different species. On the Y-axis the absolute number of microRNAs is reported, on the X-axis the name of the species. In yellow the CoGemiR high confidence (HC) prediction, in red the EnsEMBL prediction and in blue the microRNA present in miRBase.

Mentions: Overall, CoGemiR contains 5064 records – 3970 of which are annotated in miRBase, 906 are predicted by EnsEMBL and 188 are predicted by CoGemiR – distributed across 36 species, as shown in Figure 1. Furthermore, we provide direct links to miRBase and EnsEMBL, direct link to taxonomy information for all the species analyzed and direct links, whenever possible, to other relevant database, including web sites for target prediction.


CoGemiR: a comparative genomics microRNA database.

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

MicroRNAs distribution across analyzed species. The chart reports the distribution of microRNAs in different species. On the Y-axis the absolute number of microRNAs is reported, on the X-axis the name of the species. In yellow the CoGemiR high confidence (HC) prediction, in red the EnsEMBL prediction and in blue the microRNA present in miRBase.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: MicroRNAs distribution across analyzed species. The chart reports the distribution of microRNAs in different species. On the Y-axis the absolute number of microRNAs is reported, on the X-axis the name of the species. In yellow the CoGemiR high confidence (HC) prediction, in red the EnsEMBL prediction and in blue the microRNA present in miRBase.
Mentions: Overall, CoGemiR contains 5064 records – 3970 of which are annotated in miRBase, 906 are predicted by EnsEMBL and 188 are predicted by CoGemiR – distributed across 36 species, as shown in Figure 1. Furthermore, we provide direct links to miRBase and EnsEMBL, direct link to taxonomy information for all the species analyzed and direct links, whenever possible, to other relevant database, including web sites for target prediction.

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