Biomedical Engineering Reference
In-Depth Information
interaction via miRNA ID, keyword, EnsEMBL ID or genome ontology (GO)
term. Results outputted include the miRanda score, thermodynamic stability and
the statistical significance of the predicted interaction.
3.4.4
Tarbase
Tarbase (Vergoulis et al.
2011
) is a collection of supporting experimental data
for miRNA-mRNA targets covering nine organisms from a range of experimen-
tal techniques including luciferase reporter assays, high throughput sequencing and
microarrays. Version 6 of the database contains in excess of 65,000 thousand entries
generated by initially scanning the literature using a text-mining pipeline followed
by manual curation of parsed entries. Each entry contains the type of experimen-
tal technique from which the interaction was drawn, manuscript citation, alignment
of the seed region and biological relevance. Tarbase is also cross linked with other
databases including EnsEMBL and Uniprot.
3.4.5
MirTarBase
MirTarBase (Hsu et al.
2011
) is a database of 4,270 experimentally confirmed targets
for 14 species. The current build of the database (Version 2.5) covers 669 miRNAS
and 2,533 targets extracted from a total of 1,380 articles in a similar manner to
Tarbase (automatic literature mining followed by manual curation). Experimental
data is predominantly from reporter construct assays or Western blotting and to a
lesser degree from SILAC based proteomic and microarray expression profiling. The
user can conduct a species specific search for the miRNA of interest to return target
interactions. Each target interaction result contains information on the miRNA, gene
and article as well as links to complementary biological databases.
3.4.6
StarBase
Recent years have seen increased application of next-generation sequencing tech-
nologies such as HTS-clip and degradome sequencing for analysis of miRNA
mechanisms through Argonaute protein binding and transcriptional degradation. The
starBase (Yang et al.
2011
) database was developed to store the information aris-
ing from such experiments and to integrate these complex data with complementary
resources. The current build of the database contains thousands of miRNA-mRNA
interactions as well as information on Ago and other RNA binding proteins across
six organisms. The database contains a variety of tools including a genome browser,
and a search system to find interactions and integrate data with biological pathway
information such as KEGG, Biocarta and GO.
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