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Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

View ORCID ProfileMar Gonzàlez-Porta, View ORCID ProfileAlvis Brazma
doi: https://doi.org/10.1101/005967
Mar Gonzàlez-Porta
European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, United Kingdom
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Alvis Brazma
European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, United Kingdom
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Abstract

In the past years, RNA sequencing has become the method of choice for the study of transcriptome composition. When working with this type of data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes. However, the number of genes predicted to undergo differential splicing is often high, and further interpretation of the results becomes a challenging task. Here we present SwitchSeq, a novel set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes. More specifically, we provide a framework to identify switch events, i.e., cases where, for a given gene, the identity of the most abundant transcript changes across conditions. The identified events are then annotated by incorporating information from several public databases and third-party tools, and are further visualised in an intuitive manner with the independent R package tviz. All the results are displayed in a self-contained HTML document, and are also stored in txt and json format to facilitate the integration with any further downstream analysis tools. Such analysis approach can be used complementarily to Gene Ontology and pathway enrichment analysis, and can also serve as an aid in the validation of predicted changes in mRNA and protein abundance.

Availability: The latest version of SwitchSeq, including installation instructions and use cases, can be found at https://github.com/mgonzalezporta/SwitchSeq. Additionally, the plot capabilities are provided as an independent R package at https://github.com/mgonzalezporta/tviz.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 06, 2014.
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Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq
Mar Gonzàlez-Porta, Alvis Brazma
bioRxiv 005967; doi: https://doi.org/10.1101/005967
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Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq
Mar Gonzàlez-Porta, Alvis Brazma
bioRxiv 005967; doi: https://doi.org/10.1101/005967

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