GeneSet2miRNA

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract GeneSet2miRNA, a web tool which can identify significant subsets of genes from the given gene list which are the targets of a single or several miRNAs.

As input, GeneSet2miRNA accepts a list of genes.

As output, a list of miRNA-regulatory models is provided.

A miRNA-regulatory model is a group of miRNAs (single, pair, triplet or quadruplet) that is predicted to regulate a significant subset of genes from the submitted list.

There are relatively few experimentally validated miRNA-target interactions in comparison to expected numbers.

For example, the current release of the miRecords database (miRecords is an integrated resource for microRNA-target interactions) includes only 1,135 records of validated miRNA-target interactions between 301 miRNAs and 902 target genes in seven (7) animal species.

For this reason, GeneSet2miRNA is using the Predicted Targets component of the miRecords database.

The Predicted Targets component of miRecords stores predicted miRNA targets produced by eleven (11) established miRNA target prediction programs.

The sets of predicted targets vary significantly between different programs.

The manufacturer uses a very simple scoring system to arrange predictions by confidence level: the more tools that predict the interaction the better the confidence.

The manufacturer used two (2) thresholds to define each miRNAs two sets of genes.

For example, for the human genome in the first case, for each miRNA the set of genes was selected if at least 4 tools had predicted the interactions, and in the second case, if at least 5 tools predicted the interactions.

GeneSet2miRNA provides a user friendly dialog-driven submission web page and supports most available gene identifiers.

GeneSet2miRNA supports automatic analyses for several model organisms: Homo sapiens, Mus musculus and Rattus norvegicus.

Automatically supported annotations and gene Ids --

As input GeneSet2miRNA accepts several types of gene or protein identifiers.

For example, for the human genome GeneSet2miRNA supports identifiers from ‘Entrez Gene’, ‘UniProt/Swiss-Prot’, ‘Gene Symbol’, ‘UniGene’, ‘Ensembl’, ‘RefSeq Protein ID’, ‘RefSeq Transcript ID’ and ‘Affymetrix probe codes’.

Additionally a mixture of several identifier types is possible.

In the first step user supplied gene Ids are mapped to ‘Entrez Gene’ identifiers.

For this purpose files from National Center for Biotechnology Information (NCBI) and Affymetrix web sites are used.

The user gets full information on the mapping of the supplied gene ids.

The manufacturer would like to point out that protein and gene identifiers can be highly ambiguous with multiple synonymous variants.

For this reason the quality of the retrieved annotation can be different for different types of identifiers.

To escape multiple mapping issues the manufacturer recommends submitting ‘Entrez Gene’ identifies to GeneSet2miRNA.

Beyond the experimental scope --

Through example the manufacturers have demonstrated that GeneSet2miRNA can provide insight into the data that is beyond the scope of currently available experimental technologies.

It is widely accepted that miRNAs play an important role in almost all biological process.

However, the nature of such biological processes, like loss of heterozygosity (LOH) and copy number changes (CNV) in cancer cells, for example, make it almost impossible to detect experimentally, the associated miRNA activity.

The time scale of these processes and their stochastic nature makes experimental setup difficult.

Currently, the only way to explore experimentally these biological phenomena, is to conduct analyses over many cell lines to detect chromosome regions which are on average more frequently subjected to variations.

The output of such studies can be converted to genes that are located in the identified chromosome regions.

GeneSet2miRNA has been demonstrated to be able to provide 'statistically validated hypotheses' concerning which miRNAs can be related to these biological processes.

GeneSet2miRNA is one of the first web tools that employ profiling methodology to identify the signature of miRNA activity in a gene list.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site GeneSet2miRNA

Price Contact manufacturer.

G6G Abstract Number 20495

G6G Manufacturer Number 104116