Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract miRSel is a microRNA-gene association database that combines text-mining results with existing databases and computational predictions.

miRSel is resource for miRNA-gene associations and it currently offers one of the largest collections of literature derived miRNA-gene associations.

Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks.

miRSel is updated daily and can be queried via microRNA identifiers, gene/protein names, PubMed queries, and gene ontology (GO) terms.

To make sure the completeness of the miRNA-gene associations the information from the other existing databases such as:

TarBase (TarBase is a database which houses a manually curated collection of experimentally supported microRNA targets, in several animal species of central scientific interest, plants and viruses); miRecords; and

miR2Disease - (miR2Disease is a manually curated database that aims at providing a comprehensive resource of miRNA deregulation in various human diseases); has been integrated.

miRSel Web interface --

miRSel provides a web interface to retrieve information on miRNA-gene pairs stored in the database.

The interface allows you to AND-combine different options to restrict query result sets.

1) Genes can be selected based on gene names, gene symbols, protein names or database identifiers.

2) miRNAs can be selected based on miRNA identifiers and miRNA gene families.

3) A PubMed interface enables arbitrary PubMed keyword queries for searching miRSel, miRNA-gene pairs are reported only if found in PubMed abstracts matching the PubMed query.

4) The Gene Ontology (GO) option restricts the reported miRNA-gene pairs to genes associated with the selected GO-terms.

Additional filter options -

The miRSel user interface allows you to query occurrences, pairs and associations of miRNAs and genes and to restrict the entries in the database using a number of filter criteria:

1) The strictness filter enforces a strict string matching of occurrences against the dictionary entries (i.e. occurrences with special characters Not in the dictionary or wrong case are removed) (default abstract).

2) The single-sentence filter reports only miRNA and gene pairs co-occurring in single sentences as opposed to pairs co-occurring in abstracts (default none is selected).

3) The relation-type filter restricts matches to a particular type of miRNA-gene association (default none is selected).

4) The taxonomy filter aims to enforce organism specificity of the matches.

The manufacturer’s organism specific taxonomy dictionary contains synonyms and MeSH vocabularies for all examined organisms as provided by the NCBI taxonomy database.

The manufacturer’s define organism specific matches as tri-occurrences of a gene name, a miRNA name and an entry of the taxonomy dictionary (default none is selected).

5) The gene synonym filter excludes protein or gene synonyms which are assigned to multiple genes or proteins (ambiguous synonyms) in databases (default none is selected).

6) The database filter shows the text mining pairs only if they are also contained in other databases or computational predictions of miRNA gene targets (default none is selected).

miRSel Results --

As a primary query result, an annotated table of miRNA-gene pairs is presented to the user.

The table shows whether the pairs are contained in one of the manually curated databases (e.g. TarBase, miR2Disease) or if they have been predicted by miRNA-target prediction algorithms.

Besides the table view, miRNA-gene pairs can be analyzed graphically using the Graphviz software.

Both representations provide links to the primary database pages (e.g. miRBase, Entrez Gene) of the found entities and to the PubMed abstracts where the entity names have been found.

miRSel Workflow process --

After entering a complete or partial search key (e.g. a miRNA) the user can select a subset of the matching miRNAs.

Then, corresponding miRNA-target co-occurrences stored in the database are displayed in a tabular format.

This table enables the navigation to miRNA or gene pages of primary databases (e.g. miRBase, Entrez Gene, PubMed abstracts that reference particular co-occurrences, or to the database sources for which the pair has been integrated).

Also, details related to each miRNA-target pair, e.g. all possible names for a given miRNA or protein in the literature and comparison results of other databases and sequence prediction can be displayed from the table.

Finally, a miRNA target interaction graph can be displayed that also enables the navigation to miRNA and gene pages (nodes) or PubMed abstracts (edges).

System Requirements

Contact manufacturer.


Manufacturer Web Site miRSel

Price Contact manufacturer.

G6G Abstract Number 20747

G6G Manufacturer Number 104330