InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA–RNA interactions

Abstract

Abstract RNA–RNA interactions (RRI) can now be probed on a transcriptome-wide scale using proximity ligation methods such as SPLASH, PARIS, LIGR-seq, RIC-seq, and others. While individual pipelines for computationally processing the corresponding raw duplex reads exist, there is currently no method for comparing and exploring RRI networks across experimental protocols and cellular conditions. It thus remains difficult to discover biologically relevant interactions, to assess reproducibility, and to evaluate protocol-specific differences. Here, we present InteRRact - a web server for interactively exploring human RRI datasets derived from published duplex probing experiments. One key feature is that all available datasets have been processed uniformly. InteRRact visualizes intermolecular RRIs as gene-level networks and intramolecular interactions as linear, locus-specific genomic tracks. All RRIs are annotated with multiple quantitative metrics and evaluated statistically, allowing the user to readily filter interactions by strength of evidence and confidence. Moreover, any two datasets can be compared to identify shared and dataset-specific interactions across cell types, conditions, and experimental protocols. InteRRact thereby enables the discovery of biologically relevant interactions. InteRRact is available at https://e-rna.org/interract.