PlanNET: homology-based predicted interactome for multiple planarian transcriptomes

Bioinformatics. 2018 Mar 15;34(6):1016-1023. doi: 10.1093/bioinformatics/btx738.


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 The source code used is available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Gene Expression Profiling / methods*
  • Humans
  • Internet
  • Planarians / genetics*
  • Planarians / physiology
  • Protein Interaction Maps*
  • Regeneration*
  • Sequence Analysis, RNA / methods
  • Software*