PlanNET: homology-based predicted interactome for multiple planarian transcriptomes

MOTIVATION: Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein–protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities. RESULTS: We have developed a protocol to predict protein–protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms. AVAILABILITY AND IMPLEMENTATION: The web application PlanNET is available at https://compgen.bio.ub.edu/PlanNET. The source code used is available at https://compgen.bio.ub.edu/PlanNET/downloads. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.