Data sources

microRNAs

miRNA annotation

miRBase

The miRBase database is the primary online repository that stores microRNA sequence data and annotation. Every miRNA has been subjected to a extensive manual annotation effort providing a consistent and curated nomenclature for every miRNA. The current version of the database contains 18,226 microRNA precursors (genes) which correspond to 21,643 mature miRNA products, in 168 species1).

  • Release: 18
  • Last update: November 2011


Curated Databases

miRecords Validated Targets

The Validated Targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA–target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA–target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs. miRecords is expected to serve as a useful resource not only for experimental miRNA researchers, but also for informatics scientists developing the next-generation miRNA target prediction programs. The miRecords is available at http://miRecords.umn.edu/miRecords.

  • Version: 3
  • Last update: November 25, 2010


miRTarBase

miRTarBase is the largest manually curated resource of miRNA targets with experimental validation. Initially, articles related to functional studies of miRNAs are selected from PubMed and parsed using a text-mining method to detect miRNA targets. Articles containing experimentally validated interactions are reviewed manually by curators and annotated in the database. The latest version includes 4,270 interactions between 669 and 2,553 target genes in 14 species.

  • Release: 2.5
  • Last update: October 15, 2011


Non-curated Databases

  • Release: August 2010
  • Last update: August 2010
  • Release: 6.0
  • Last update: November 2011


Disease Databases

  • Release: November 2011
  • Last update: November 1, 2011


  • Release: 2.0
  • Last update: January 2010


Transcription Factors

  • ENCODE Project data
  • Data grathered through Ensembl's Perl API.
  • Release: 64 (GRCh37)

Statistics

microRNAs Transcription factors
microRNAs Transcription factors
 Venn Diagram miRNAs

Data generation

The information on TFBSs and miRNA target sites has been collected from different databases. This information is currently available for human and mouse, but soon new species will be added.

microRNAs

Correspondences between miRNA genes (precursors) and miRNA mature sequences, along with other interesting annotation details were extracted from miRBase database. Four miRNA-target databases have been selected to represent this kind of interactions, two curated, experimentally-based resources (miRTarBase and miRecords Validated targets) and two computationally predicted repositories of miRNA-gene interactions (TargetScan and microrna.org).

In the Database selection of the RENATO form, users can choose one of the 3 options related with miRNAs:

  • Curated: Corresponding to unique interactions after joining miRTarBase and miRecords.
  • Computational predictions: predicted miRNA-gene interactions from TargetScan and microrna.org.
  • All databases: Unique interactions after joining all both, curated and computational predictions of miRNA-gene relationships.

Human annotated relationships between miRNAs and diseases have been down loaded from The human microRNA disease database (HMDD). Besides, we have also included human and mouse information provided by PhenomiR which includes phenotypes and diseases annotated to miRNAs.

Transcription Factor Binding Sites (TFBSs)

Information on TFBSs was taken from Ensembl through the corresponding Perl API. This data has been incorporated based on Chromatin immunoprecipitation (ChIP)-chip and ChIP-Seq experiments undertaken by the ENCODE project (more information at Ensembl's Regulatory build section). We have mapped the provided TFBSs to the promoter region (-2500bp to +500bp of the Transcription Start Site) of a gene, establishing this way the relationship TF-gene.

databases.txt · Last modified: 2012/05/03 14:59 by mbleda
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