RT Journal Article
SR Electronic
T1 psichomics: graphical application for alternative splicing quantification and analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 261180
DO 10.1101/261180
A1 Nuno Saraiva-Agostinho
A1 Nuno L. Barbosa-Morais
YR 2018
UL http://biorxiv.org/content/early/2018/02/20/261180.abstract
AB Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global studies of alternative splicing in different physiological and disease contexts. However, current bioinformatics tools for alternative splicing analysis from RNA-seq data are not user-friendly, disregard available exon-exon junction quantification or have limited downstream analysis features. To overcome such limitations, we have developed psichomics, an R package with an intuitive graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression project and user-provided data. These integrative analyses can also incorporate clinical and molecular sample-associated features. We successfully used psichomics to reveal alternative splicing signatures specific to stage I breast cancer and associated novel putative prognostic factors.