2026-06-02T02:57:42Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/72632023-03-17T11:54:10Zcom_10259_3847com_10259_5086com_10259_2604col_10259_7109

Urda Muñoz, Daniel Aragón, Francisco Bautista, Rocío Franco, Leonardo Veredas, Francisco J. Claros, Manuel Gonzalo Jerez, José Manuel 2023-01-18T08:00:34Z 2023-01-18T08:00:34Z 2018 1752-0509 http://hdl.handle.net/10259/7263 s12918-018-0612-8 In RNA-Seq gene expression analysis, a genetic signature or biomarker is defined as a subset of genes that is probably involved in a given complex human trait and usually provide predictive capabilities for that trait. The discovery of new genetic signatures is challenging, as it entails the analysis of complex-nature information encoded at gene level. Moreover, biomarkers selection becomes unstable, since high correlation among the thousands of genes included in each sample usually exists, thus obtaining very low overlapping rates between the genetic signatures proposed by different authors. In this sense, this paper proposes BLASSO, a simple and highly interpretable linear model with l1-regularization that incorporates prior biological knowledge to the prediction of breast cancer outcomes. Two different approaches to integrate biological knowledge in BLASSO, Gene-specific and Gene-disease, are proposed to test their predictive performance and biomarker stability on a public RNA-Seq gene expression dataset for breast cancer. The relevance of the genetic signature for the model is inspected by a functional analysis. Trabajo presentado en: V International Work-Conference on Bioinformatics and Biomedical Engineering Publication of this manuscript was sponsored by TIN2017-88728-C2 grant. application/pdf eng Springer Nature BMC Systems Biology. 2018, V. 12, n. 5, p. 14-26 https://doi.org/10.1186/s12918-018-0612-8 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2017-88728-C2-1-R/ES/AVANCES EN EL DISEÑO Y ADAPTACION DE ALGORITMOS DE APRENDIZAJE PROFUNDO PARA SU APLICACION A PROBLEMAS EN LAS AREAS DE BIOMEDICINA Y CONTAMINACION ATMOSFERICA/ Atribución 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess RNA-Seq Biomarkers selection Biological knowledge Machine learning Precision medicine Informática Biología molecular Computer science Molecular biology BLASSO: integration of biological knowledge into a regularized linear model info:eu-repo/semantics/conferenceObject info:eu-repo/semantics/publishedVersion BMC Systems Biology 12 5 14 26