info:eu-repo/semantics/article
Differential splicing analysis based on isoforms expression with NBSplice
Fecha
2020-03Registro en:
Merino, Gabriela Alejandra; Fernandez, Elmer Andres; Differential splicing analysis based on isoforms expression with NBSplice; Academic Press Inc Elsevier Science; Journal Of Biomedical Informatics; 103; 3-2020; 103378-1/11
1532-0464
CONICET Digital
CONICET
Autor
Merino, Gabriela Alejandra
Fernandez, Elmer Andres
Resumen
Alternative splicing alterations have been widely related to several human diseases revealing the importance of their study for the success of translational medicine. Differential splicing (DS) occurrence has been mainly analyzed through exon-based approaches over RNA-seq data. Although these strategies allow identifying differentially spliced genes, they ignore the identity of the affected gene isoforms which is crucial to understand the underlying pathological processes behind alternative splicing changes. Moreover, despite several isoform quantification tools for RNA-seq data have been recently developed, DS tools have not taken advantage of them. Here, the NBSplice R package for differential splicing analysis by means of isoform expression data is presented. It estimates differences on relative expressions of gene transcripts between experimental conditions to infer changes in gene alternative splicing patterns. The developed tool was evaluated using a synthetic RNA-seq dataset with controlled differential splicing. NBSplice accurately predicted DS occurrence, outperforming current methods in terms of accuracy, sensitivity, F-score, and false discovery rate control. The usefulness of our development was demonstrated by the analysis of a real cancer dataset, revealing new differentially spliced genes that could be studied pursuing new colorectal cancer biomarkers discovery.