microGraphite

miRNAs have been extensively studied and hundreds of target genes have been found. However, despite all these efforts, signaling pathways that are the formal description of biological circuits, contain very few miRNAs. This penalizes pathway analyses, widely used and essential approaches to enhance transcriptome measurements interpretations.

To overcome this limitation we developed micrographite, an R pipeline able to integrate pathway information with predicted and validated miRNA–target interactions and to perform integrated topological analyses of miRNA and gene expression profiles to identify miRNA–gene circuits.

Calura E, Martini P, Sales G, Beltrame L, Chiorino G, D’Incalci M, Marchini S, Romualdi C. Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles. Nucleic Acids Res. 2014 Jun;42(11):e96. doi: 10.1093/nar/gku354.