A comparison of mechanistic signaling pathway activity analysis methods

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• dc.contributor.author Amadoz, Alicia
• dc.contributor.author Hidalgo, Marta R.
• dc.contributor.author Çubut, Cankut
• dc.contributor.author Carbonell-Caballero, Jose
• dc.contributor.author Dopazo, Joaquín
• dc.date.accessioned 2020-03-18T07:47:51Z
• dc.date.available 2020-03-18T07:47:51Z
• dc.date.issued 2019
• dc.description.abstract Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human traits, whereas conventional pathway enrichment approaches produce only illustrative results of limited practical utility. Recently, a family of new methods has emerged that change the focus from the whole pathways to the definition of elementary subpathways within them that have any mechanistic significance and to the study of their activities. Thus, mechanistic pathway activity (MPA) methods constitute a new paradigm that allows recoding poorly informative genomic measurements into cell activity quantitative values and relate them to phenotypes. Here we provide a review on the MPA methods available and explain their contribution to systems medicine approaches for addressing challenges in the diagnostic and treatment of complex diseases.
• dc.description.sponsorship This work was supported by grants SAF2017-88908-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, both co-funded with European Regional Development Funds (ERDF), and EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559).
• dc.format.mimetype application/pdf
• dc.identifier.citation Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Brief Bioinform. 2019; 20(5):1655-68. DOI: 10.1093/bib/bby040
• dc.identifier.doi http://dx.doi.org/10.1093/bib/bby040
• dc.identifier.issn 1467-5463
• dc.identifier.uri http://hdl.handle.net/10230/43928
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Brief Bioinform. 2019; 20(5):1655-68
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/SAF2017-88908-R
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
• dc.rights © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword Disease mechanism
• dc.subject.keyword Mathematical models
• dc.subject.keyword Networks
• dc.subject.keyword Signaling pathways
• dc.subject.keyword Systems biology
• dc.subject.keyword Transcriptomics
• dc.title A comparison of mechanistic signaling pathway activity analysis methods
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion