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...

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Detalles Bibliográficos
Autores: Castillo-Lara, Sergio, Abril Ferrando, Josep Francesc, 1970-
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2017
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/195344
Acceso en línea:https://hdl.handle.net/2445/195344
Access Level:acceso abierto
Palabra clave:Planària (Gènere)
RNA
Planaria (Genus)
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repository_id_str
spelling PlanNET: homology-based predicted interactome for multiple planarian transcriptomesCastillo-Lara, SergioAbril Ferrando, Josep Francesc, 1970-Planària (Gènere)RNAPlanaria (Genus)RNAMotivation: 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.Oxford University Press2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfhttps://hdl.handle.net/2445/195344Articles publicats en revistes (Genètica, Microbiologia i Estadística)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésVersió postprint del document publicat a: https://doi.org/10.1093/bioinformatics/btx738Bioinformatics, 2017, vol. 34, num. 6, p. 1016-1023https://doi.org/10.1093/bioinformatics/btx738(c) Castillo-Lara, Sergio et al., 2017info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1953442026-05-27T06:46:51Z
dc.title.none.fl_str_mv PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
title PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
spellingShingle PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
Castillo-Lara, Sergio
Planària (Gènere)
RNA
Planaria (Genus)
RNA
title_short PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
title_full PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
title_fullStr PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
title_full_unstemmed PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
title_sort PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
dc.creator.none.fl_str_mv Castillo-Lara, Sergio
Abril Ferrando, Josep Francesc, 1970-
author Castillo-Lara, Sergio
author_facet Castillo-Lara, Sergio
Abril Ferrando, Josep Francesc, 1970-
author_role author
author2 Abril Ferrando, Josep Francesc, 1970-
author2_role author
dc.subject.none.fl_str_mv Planària (Gènere)
RNA
Planaria (Genus)
RNA
topic Planària (Gènere)
RNA
Planaria (Genus)
RNA
description 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.
publishDate 2017
dc.date.none.fl_str_mv 2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/195344
url https://hdl.handle.net/2445/195344
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1093/bioinformatics/btx738
Bioinformatics, 2017, vol. 34, num. 6, p. 1016-1023
https://doi.org/10.1093/bioinformatics/btx738
dc.rights.none.fl_str_mv (c) Castillo-Lara, Sergio et al., 2017
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Castillo-Lara, Sergio et al., 2017
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv Articles publicats en revistes (Genètica, Microbiologia i Estadística)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300719

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