Identification and visualization of differential isoform expression in RNA-seq time series
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Título: | Identification and visualization of differential isoform expression in RNA-seq time series |
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Autor/es: | Nueda, María José | Martorell-Marugan, Jordi | Martí, Cristina | Tarazona, Sonia | Conesa, Ana |
Grupo/s de investigación o GITE: | Bioquímica Aplicada/Applied Biochemistry (AppBiochem) | Sistemas Dinámicos y Estadística (SISDINEST) |
Centro, Departamento o Servicio: | Universidad de Alicante. Departamento de Matemáticas |
Palabras clave: | Isoform expression | RNA-seq time series | Identification | Visualization |
Área/s de conocimiento: | Estadística e Investigación Operativa |
Fecha de publicación: | 1-feb-2018 |
Editor: | Oxford University Press |
Cita bibliográfica: | Bioinformatics. 2018, 34(3): 524-526. doi:10.1093/bioinformatics/btx578 |
Resumen: | Motivation: As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Results: Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. Availability and implementation: The package is freely available under the LGPL license from the Bioconductor web site. |
Patrocinador/es: | This work was supported by EU FP7 STATegra project agreement [306000]; and the Spanish Ministry of Economy and Competitiveness [BIO2012-40244 and BIO2015-71658-R]. |
URI: | http://hdl.handle.net/10045/73174 |
ISSN: | 1367-4803 (Print) | 1460-2059 (Online) |
DOI: | 10.1093/bioinformatics/btx578 |
Idioma: | eng |
Tipo: | info:eu-repo/semantics/article |
Derechos: | © The Author 2017. 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. |
Revisión científica: | si |
Versión del editor: | http://dx.doi.org/10.1093/bioinformatics/btx578 |
Aparece en las colecciones: | INV - SISDINEST - Artículos de Revistas INV - AppBiochem - Artículos de Revistas Investigaciones financiadas por la UE INV - GESTA - Artículos de Revistas |
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