GUILDify v2.0: a tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets
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- dc.contributor.author Aguirre Plans, Joaquim, 1993-
- dc.contributor.author Piñero González, Janet, 1977-
- dc.contributor.author Sanz, Ferran
- dc.contributor.author Furlong, Laura I., 1971-
- dc.contributor.author Fernández Fuentes, Narcís
- dc.contributor.author Oliva Miguel, Baldomero
- dc.contributor.author Guney, Emre
- dc.date.accessioned 2020-02-14T08:24:52Z
- dc.date.issued 2019
- dc.description.abstract The genetic basis of complex diseases involves alterations on multiple genes. Unraveling the interplay between these genetic factors is key to the discovery of new biomarkers and treatments. In 2014, we introduced GUILDify, a web server that searches for genes associated to diseases, finds novel disease genes applying various network-based prioritization algorithms and proposes candidate drugs. Here, we present GUILDify v2.0, a major update and improvement of the original method, where we have included protein interaction data for seven species and 22 human tissues and incorporated the disease-gene associations from DisGeNET. To infer potential disease relationships associated with multi-morbidities, we introduced a novel feature for estimating the genetic and functional overlap of two diseases using the top-ranking genes and the associated enrichment of biological functions and pathways (as defined by GO and Reactome). The analysis of this overlap helps to identify the mechanistic role of genes and protein-protein interactions in comorbidities. Finally, we provided an R package, guildifyR, to facilitate programmatic access to GUILDify v2.0 (http://sbi.upf.edu/guildify2).
- dc.description.sponsorship The authors received support from the following:ISCIII–FEDER (PI13/00082, CP10/00524, CPII16/00026); IMI-JU under grants agreements no. 116030(TransQST) and no. 777365 (eTRANSAFE), re-sources of which are composed of financial contribu-tion from the EU-FP7 (FP7/2007- 2013) and EFPIAcompanies in kind contribution; the EU H2020Programme 2014–2020 under grant agreementsno. 634143 (MedBioinformatics) and no. 676559(Elixir-Excelerate); the Spanish Ministry of Economy(MINECO) (BIO2017-85329-R, RYC-2015-17519);and“Unidad de Excelencia María de Maeztu,”fundedby the Spanish Ministry of Economy (ref.: MDM-2014-0370). The Research Programme on BiomedicalInformatics is a member of the Spanish NationalBioinformatics Institute, PRB2-ISCIII, and is supportedby Grant PT13/0001/0023 of the PE I+D+i 2013-2016funded by ISCIII and FEDER
- dc.format.mimetype application/pdf
- dc.identifier.citation Aguirre-Plans J, Piñero J, Sanz F, Furlong LI, Fernandez-Fuentes N, Oliva B et al. GUILDify v2.0: a tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets. J Mol Biol. 2019;431(13):2477-84. DOI: 10.1016/j.jmb.2019.02.027
- dc.identifier.doi http://dx.doi.org/10.1016/j.jmb.2019.02.027
- dc.identifier.issn 0022-2836
- dc.identifier.uri http://hdl.handle.net/10230/43598
- dc.language.iso eng
- dc.publisher Elsevier
- dc.relation.ispartof Journal of Molecular Biology. 2019;431(13):2477-84
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/116030
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/634143
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/777365
- dc.rights © Elsevier http://dx.doi.org/10.1016/j.jmb.2019.02.027
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.keyword Disease comorbidity
- dc.subject.keyword Drug repurposing
- dc.subject.keyword Network analysis
- dc.subject.keyword Systems medicine
- dc.subject.keyword Target prioritization
- dc.title GUILDify v2.0: a tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion