gsa4mirna – Integrated gene set analysis for microRNA studies

Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.

Here, researchers from CIPF, Spain propose an enhanced methodology that builds on the well-established gene set analysis paradigm. Evidence for differential expression at the miRNA level is transferred to a gene differential inhibition score which is easily interpretable in terms of gene sets or pathways. Such transferred indexes account for the additive effect of several miRNAs targeting the same gene, and also incorporate cancellation effects between cases and controls. Together, these two desirable characteristics allow for more accurate modeling of regulatory processes.

The researchers analyze high-throughput sequencing data from 20 different cancer types and provide exhaustive reports of gene and Gene Ontology-term deregulation by miRNA action.


Interpretation of the differential expression statistic at miRNA level and the transferred index at gene level

Availability – The proposed methodology was implemented in the Bioconductor library mdgsa For the purpose of reproducibility all of the scripts are available at

Garcia-Garcia F, Panadero J, Dopazo J, Montaner D. (2016) Integrated gene set analysis for microRNA studies. Bioinformatics [Epub ahead of print]. [article]

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