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http://hdl.handle.net/2445/195344
Title: | PlanNET: homology-based predicted interactome for multiple planarian transcriptomes |
Author: | Castillo-Lara, Sergio Abril Ferrando, Josep Francesc, 1970- |
Keywords: | Planària (Gènere) RNA Planaria (Genus) RNA |
Issue Date: | 24-Nov-2017 |
Publisher: | Oxford University Press |
Abstract: | 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 eleven 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: 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. |
Note: | Versió postprint del document publicat a: https://doi.org/10.1093/bioinformatics/btx738 |
It is part of: | Bioinformatics, 2017, vol. 34, num. 6, p. 1016-1023 |
URI: | http://hdl.handle.net/2445/195344 |
Related resource: | https://doi.org/10.1093/bioinformatics/btx738 |
ISSN: | 1367-4803 |
Appears in Collections: | Articles publicats en revistes (Genètica, Microbiologia i Estadística) |
Files in This Item:
File | Description | Size | Format | |
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677217.pdf | 1.53 MB | Adobe PDF | View/Open |
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