comoRbidity: an R package for the systematic analysis of disease comorbidities

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  • dc.contributor.author Gutiérrez Sacristán, Alba
  • dc.contributor.author Bravo Serrano, Àlex, 1984-
  • dc.contributor.author Giannoula, Alexia
  • dc.contributor.author Mayer, Miguel Ángel, 1960-
  • dc.contributor.author Sanz, Ferran
  • dc.contributor.author Furlong, Laura I., 1971-
  • dc.date.accessioned 2018-11-30T11:40:37Z
  • dc.date.available 2018-11-30T11:40:37Z
  • dc.date.issued 2018
  • dc.description.abstract MOTIVATION: The study of comorbidities is a major priority due to their impact on life expectancy, quality of life and healthcare cost. The availability of electronic health records (EHRs) for data mining offers the opportunity to discover disease associations and comorbidity patterns from the clinical history of patients gathered during routine medical care. This opens the need for analytical tools for detection of disease comorbidities, including the investigation of their underlying genetic basis. RESULTS: We present comoRbidity, an R package aimed at providing a systematic and comprehensive analysis of disease comorbidities from both the clinical and molecular perspectives. comoRbidity leverages from (i) user provided clinical data from EHR databases (the clinical comorbidity analysis) and (ii) genotype-phenotype information of the diseases under study (the molecular comorbidity analysis) for a comprehensive analysis of disease comorbidities. The clinical comorbidity analysis enables identifying significant disease comorbidities from clinical data, including sex and age stratification and temporal directionality analyses, while the molecular comorbidity analysis supports the generation of hypothesis on the underlying mechanisms of the disease comorbidities by exploring shared genes among disorders. The open-source comoRbidity package is a software tool aimed at expediting the integrative analysis of disease comorbidities by incorporating several analytical and visualization functions.
  • dc.description.sponsorship The authors received support from ISCIII-FEDER (PI13/00082, CP10/00524, CPII16/00026), IMI-JU under grants agreements no. 115372 (EMIF), no. 115735 (iPiE), resources of which are composed of financial contribution from the EU-FP7 (FP7/2007-2013) and EFPIA companies in kind contribution and the EU H2020 Programme 2014–2020 under grant agreements no. 634143 (MedBioinformatics) and no. 676559 (ElixirExcelerate). The Research Programme on Biomedical Informatics (GRIB) is a member of the Spanish National Bioinformatics Institute (INB), PRB2-ISCIII and is supported by grant PT13/0001/0023, of the PE I + D+i 2013-2016, funded by ISCIII and FEDER. AGS acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the ‘María de Maeztu’ Programme for Units of Excellence in R&D (MDM-2014-0370).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Gutiérrez-Sacristán A, Bravo À, Giannoula A, Mayer MA, Sanz F, Furlong LI. comoRbidity: an R package for the systematic analysis of disease comorbidities. Bioinformatics. 2018;34(18):3228-30. DOI: 10.1093/bioinformatics/bty315
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/bty315
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/35919
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Bioinformatics. 2018;34(18):3228-30
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/634143
  • 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.title comoRbidity: an R package for the systematic analysis of disease comorbidities
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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