PlanNET: homology-based predicted interactome for multiple planarian transcriptomes

• DOI: 10.1093/bioinformatics/btx738
• Publication Date: 2017-11-23T20:16:26Z
• Authors: S Castillo-Lara; J F Abril
• Keywords: Interactome; Planarian

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