Factors affecting interactome-based prediction of human genes associated with clinical signs

[Background] Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clini...

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Detalhes bibliográficos
Autores: González-Pérez, Sara, Pazos, Florencio, Chagoyen, Mónica
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/153395
Acesso em linha:http://hdl.handle.net/10261/153395
Access Level:acceso abierto
Palavra-chave:Gene prioritization
Human interactome
Clinical signs
Network-based methods
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spelling Factors affecting interactome-based prediction of human genes associated with clinical signsGonzález-Pérez, SaraPazos, FlorencioChagoyen, MónicaGene prioritizationHuman interactomeClinical signsNetwork-based methods[Background] Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome.[Results] Our analysis reveals that these approaches can locate genes associated with clinical signs with variable performance that depends on the sign and associated disease. We analyzed several clinical and biological factors that explain these variable results, including number of genes involved (mono- vs. oligogenic diseases), mode of inheritance, type of clinical sign and gene product function.[Conclusions] Our results indicate that the characteristics of the clinical signs and their related diseases should be considered for interpreting the results of network-prediction methods, such as those aimed at discovering disease-related genes and variants. These results are important due the increasing use of clinical signs as an alternative to diseases for studying the molecular basis of human pathologies.This work has been partially funded by the Spanish Ministry of Economy and Competitiveness (Ministerio de Economía y Competividad) through grant SAF2016–78041-C2–2-R. We acknowledge support of the publication fee by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).Peer reviewedBioMed CentralMinisterio de Economía y Competitividad (España)CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2017201720172017info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/153395reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SAF2016–78041-C2–2-Rhttp://dx.doi.org/10.1186/s12859-017-1754-1Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1533952026-05-22T06:33:51Z
dc.title.none.fl_str_mv Factors affecting interactome-based prediction of human genes associated with clinical signs
title Factors affecting interactome-based prediction of human genes associated with clinical signs
spellingShingle Factors affecting interactome-based prediction of human genes associated with clinical signs
González-Pérez, Sara
Gene prioritization
Human interactome
Clinical signs
Network-based methods
title_short Factors affecting interactome-based prediction of human genes associated with clinical signs
title_full Factors affecting interactome-based prediction of human genes associated with clinical signs
title_fullStr Factors affecting interactome-based prediction of human genes associated with clinical signs
title_full_unstemmed Factors affecting interactome-based prediction of human genes associated with clinical signs
title_sort Factors affecting interactome-based prediction of human genes associated with clinical signs
dc.creator.none.fl_str_mv González-Pérez, Sara
Pazos, Florencio
Chagoyen, Mónica
author González-Pérez, Sara
author_facet González-Pérez, Sara
Pazos, Florencio
Chagoyen, Mónica
author_role author
author2 Pazos, Florencio
Chagoyen, Mónica
author2_role author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Gene prioritization
Human interactome
Clinical signs
Network-based methods
topic Gene prioritization
Human interactome
Clinical signs
Network-based methods
description [Background] Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome.
publishDate 2017
dc.date.none.fl_str_mv 2017
2017
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/153395
url http://hdl.handle.net/10261/153395
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SAF2016–78041-C2–2-R
http://dx.doi.org/10.1186/s12859-017-1754-1
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812455

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