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http://hdl.handle.net/2445/195344
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DC Field | Value | Language |
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dc.contributor.author | Castillo-Lara, Sergio | - |
dc.contributor.author | Abril Ferrando, Josep Francesc, 1970- | - |
dc.date.accessioned | 2023-03-15T18:25:50Z | - |
dc.date.available | 2023-03-15T18:25:50Z | - |
dc.date.issued | 2017-11-24 | - |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://hdl.handle.net/2445/195344 | - |
dc.description.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. | - |
dc.format.extent | 8 p. | - |
dc.format.mimetype | application/pdf | - |
dc.language.iso | eng | - |
dc.publisher | Oxford University Press | - |
dc.relation.isformatof | Versió postprint del document publicat a: https://doi.org/10.1093/bioinformatics/btx738 | - |
dc.relation.ispartof | Bioinformatics, 2017, vol. 34, num. 6, p. 1016-1023 | - |
dc.relation.uri | https://doi.org/10.1093/bioinformatics/btx738 | - |
dc.rights | (c) Castillo-Lara, Sergio et al., 2017 | - |
dc.source | Articles publicats en revistes (Genètica, Microbiologia i Estadística) | - |
dc.subject.classification | Planària (Gènere) | - |
dc.subject.classification | RNA | - |
dc.subject.other | Planaria (Genus) | - |
dc.subject.other | RNA | - |
dc.title | PlanNET: homology-based predicted interactome for multiple planarian transcriptomes | - |
dc.type | info:eu-repo/semantics/article | - |
dc.type | info:eu-repo/semantics/acceptedVersion | - |
dc.identifier.idgrec | 677217 | - |
dc.date.updated | 2023-03-15T18:25:50Z | - |
dc.rights.accessRights | info:eu-repo/semantics/openAccess | - |
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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