psichomics: graphical application for alternative splicing quantification and analysis

Abstract 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 stud...

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Bibliographic Details
Published in:Nucleic acids research 2019-01, Vol.47 (2), p.e7-e7
Main Authors: Saraiva-Agostinho, Nuno, Barbosa-Morais, Nuno L
Format: Article
Language:English
Subjects:
Alternative Splicing
Breast Neoplasms - genetics
Breast Neoplasms - mortality
Computer Graphics
Female
Gene Expression
Humans
Methods Online
Software
Survival Analysis
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Summary:Abstract 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, the Sequence Read Archive project and user-provided data. These integrative analyses can also incorporate clinical and molecular sample-associated features. We successfully used psichomics in a laptop to reveal alternative splicing signatures specific to stage I breast cancer and associated novel putative prognostic factors.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gky888