Analysis of alternative splicing events in custom gene datasets by AStalavista.

TitleAnalysis of alternative splicing events in custom gene datasets by AStalavista.
Publication TypeJournal Article
Year of Publication2015
AuthorsFoissac, S, Sammeth, M
JournalMethods Mol Biol
Volume1269
Pagination379-92
Date Published2015
ISSN1940-6029
KeywordsAlternative Splicing, Computational Biology, High-Throughput Nucleotide Sequencing, Humans, Transcriptome
Abstract

Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process is highly regulated and makes up a large part of the differences between species, cell types, and states. The key to compare AS across different genes or organisms is to tokenize the AS phenomenon into atomary units, so-called AS events. These events then usually are grouped by common patterns to investigate the underlying molecular mechanisms that drive their regulation. However, attempts to decompose loci with AS observations into events are often hampered by applying a limited set of a priori defined event patterns which are not capable to describe all AS configurations and therefore cannot decompose the phenomenon exhaustively. In this chapter, we describe working scenarios of AStalavista, a computational method that reports all AS events reflected by transcript annotations. We show how to practically employ AStalavista to study AS variation in complex transcriptomes, as characterized by the human GENCODE annotation. Our examples demonstrate how the inherent and universal AStalavista paradigm allows for an automatic delineation of AS events in custom gene datasets. Additionally, we sketch an example of an AStalavista use case including next-generation sequencing data (RNA-Seq) to enrich the landscape of discovered AS events.

DOI10.1007/978-1-4939-2291-8_24
Alternate JournalMethods Mol. Biol.
PubMed ID25577392