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Toxo: A Library for Calculating Penetrance Tables of High-Order Epistasis Models
dc.contributor.author | Ponte-Fernández, Christian | |
dc.contributor.author | González-Domínguez, Jorge | |
dc.contributor.author | Carvajal-Rodriguez, Antonio | |
dc.contributor.author | Martín, María J. | |
dc.date.accessioned | 2020-04-24T14:40:41Z | |
dc.date.available | 2020-04-24T14:40:41Z | |
dc.date.issued | 2020-04-09 | |
dc.identifier.citation | Ponte-Fernández, C., González-Domínguez, J., Carvajal-Rodríguez, A. et al. Toxo: a library for calculating penetrance tables of high-order epistasis models. BMC Bioinformatics 21, 138 (2020). Doi: 10.1186/s12859-020-3456-3 | es_ES |
dc.identifier.issn | 1471-2105 | |
dc.identifier.uri | http://hdl.handle.net/2183/25427 | |
dc.description.abstract | [Abstract] Background Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations. Results Toxo is a MATLAB library designed to calculate penetrance tables of epistasis models of any interaction order which resemble real data more closely. The user specifies the desired heritability (or prevalence) and the program maximizes the table’s prevalence (or heritability) according to the input epistatic model boundaries. Conclusions Toxo extends the capabilities of existing simulators that define epistasis using penetrance tables. These tables can be directly used as input for software simulators such as GAMETES so that they are able to generate data samples with larger interactions and more realistic prevalences/heritabilities. | es_ES |
dc.description.sponsorship | This research was supported by the Ministry of Economy and Competitiveness of Spain (CGL2016-75482-P), the Ministry of Economy and Competitiveness of Spain and FEDER funds of the EU (TIN2016-75845-P), the Xunta de Galicia (Grupo de Referencia Competitiva, ED431C2016-037), the Xunta de Galicia and FEDER funds of the EU (Centro de Investigación de Galicia accreditation 2019-2022, ref. ED431G2019/01), Consolidation Program of Competitive Research (ED431C 2017/04) and the FPU Program of the Ministry of Education of Spain (FPU16/01333) | es_ES |
dc.description.sponsorship | Xunta de Galicia; ED431C2016-037 | es_ES |
dc.description.sponsorship | Xunta de Galicia; ED431G2019/01 | es_ES |
dc.description.sponsorship | Xunta de Galicia; ED431C 2017/04 | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | BioMed Central Ltd. | es_ES |
dc.relation | info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2016-75482-P/ES/CAUSAS Y CONSECUENCIAS DE LA EVOLUCION DE LA PREFERENCIA EN LA ELECCION DE PAREJA EN POBLACIONES NATURALES | |
dc.relation | info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-75845-P/ES/NUEVOS DESAFIOS EN COMPUTACION DE ALTAS PRESTACIONES: DESDE ARQUITECTURAS HASTA APLICACIONES (II) | |
dc.relation | info:eu-repo/grantAgreement/MECD/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FPU16%2F01333/ES/ | |
dc.relation | info:eu-repo/grantAgreement/MECD/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FPU16%2F01333/ES/ | |
dc.relation | info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-75845-P/ES/NUEVOS DESAFIOS EN COMPUTACION DE ALTAS PRESTACIONES: DESDE ARQUITECTURAS HASTA APLICACIONES (II) | |
dc.relation | info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2016-75482-P/ES/CAUSAS Y CONSECUENCIAS DE LA EVOLUCION DE LA PREFERENCIA EN LA ELECCION DE PAREJA EN POBLACIONES NATURALES | |
dc.relation.uri | https://doi.org/10.1186/s12859-020-3456-3 | es_ES |
dc.rights | Atribución 4.0 Internacional (CC BY 4.0) | es_ES |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Simulation | es_ES |
dc.subject | Epistasis model | es_ES |
dc.subject | Gene interaction | es_ES |
dc.subject | Penetrance | es_ES |
dc.subject | Prevalence | es_ES |
dc.subject | Heritability | es_ES |
dc.title | Toxo: A Library for Calculating Penetrance Tables of High-Order Epistasis Models | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.rights.access | info:eu-repo/semantics/openAccess | es_ES |
UDC.journalTitle | BMC Bioinformatics | es_ES |
UDC.volume | 21 | es_ES |
dc.identifier.doi | 10.1186/s12859-020-3456-3 |
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