Journal Article

RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions

Chasles, Simon, Lemaire, Mélanie, Major, François, Gaillard-Duchassin, Zakary, Quenneville, Jordan, Gagnon, Etienne

2026

Overview

RIMap-RISC is a web-accessible database for transcriptome-wide modeling of human microRNA (miRNA) targeting. It computes plausible transcript-miRNA interactions and records their position, duplex secondary structure, free energy, site classification, dissociation constant, target accessibility, and evolutionary conservation. RIMap-RISC supports transcript-wide queries and allows users to explore and export interaction data through an interactive interface or RESTful API programmatic access. Unlike existing tools, RIMap-RISC integrates duplex-structure prediction within a biophysical framework modeling the bipartite architecture of RISC, accommodating a bridge between seed and supplementary pairing. A novel, unambiguous, miRNA-centric nomenclature for interaction types is also introduced.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Data models / Databases, Genetic / Dissociation constants / Evolutionary Biology / Evolutionary conservation / Free energy / Human Genetics / Humans / Life Sciences / Microbial Genetics and Genomics / MicroRNA targeting / MicroRNAs / MicroRNAs - chemistry / MicroRNAs - genetics / MicroRNAs - metabolism / miRNA / Nomenclature / Nucleic Acid Conformation / Plant Genetics and Genomics / Post-transcriptional regulation / Protein structure / Proteins / RNA accessibility / RNA duplex structure / Secondary structure / Software / Transcriptome / Transcriptome-wide analysis / Transcriptomes