mirTissue: A web service that characterizes the type of miRNA-target interaction in specific tissues.

Motivation

Nowadays, the regulatory role of microRNAs (miRNAs) is evident in both physiological and pathological processes such as tumors.

Bioinformatics approaches, as miRNA-target interaction prediction tools, give a big contribute in helping the comprehension of molecular mechanisms involved in these pathologies. However, there is a lacking in defining these molecular interactions in a tissue-specific context.

mirTissue is a web service based on validated miRNA-target interactions linked to a specific tissue context, specifically related to cancer pathologies, in order to: 1) characterize the most significant interactions related to a specific tissue; 2) understand the mechanism of action that mirrors, whether through messenger degradation or translation inhibition.

Methods

Expression values of both miRNA and mRNA, belonging to 15 types of tumor tissues, were downloaded from TCGA database. In order to characterize a miRNA-target interaction with respect to a particular tissue, we computed, by means of the global test, the correlation between miRNA and corresponding mRNA (target) expression. The sign of the correlation, in fact, can provide an insight about the presence, or less, of an interaction in a specific tissue. In particular, anti-correlation means the likely existence of an interaction (degradation). In case of correlation, we considered the protein expression value (if any) of the interested mRNA, because an anti-correlation between gene and protein expression can likely be related to a miRNA-target interaction causing translation inhibition.

mirTissue web service is available here.