Wiring miRNAs to pathways: A topological approach to integrate miRNA and mRNA expression profiles

Enrica Calura, Paolo Martini, Gabriele Sales, Luca Beltrame, Giovanna Chiorino, Maurizio D'Incalci, Sergio Marchini, Chiara Romualdi

Research output: Contribution to journalArticlepeer-review

Abstract

The production rate of gene expression data is nothing less than astounding. However, with the benefit of hindsight we can assert that, since we completely ignored the non-coding part of the transcriptome, we spent the last decade to study cell mechanisms having few data in our hands. In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention. Given the state of knowledge about their biogenesis, mechanisms of action and the numerous experimentally validated target genes, miRNAs are also gradually appearing in the formal pathway representations such as KEGG and Reactome maps. However, the number of miRNAs annotated in pathway maps are very few and pathway analyses exploiting this new regulatory layer are still lacking. To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles. Here, micrographite is used to study and dissect the epithelial ovarian cancer gene and miRNA transcriptome defining and validating a new regulatory circuit related to ovarian cancer histotype specificity.

Original languageEnglish
JournalNucleic Acids Research
Volume42
Issue number11
DOIs
Publication statusPublished - 2014

ASJC Scopus subject areas

  • Genetics

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