Analysis of differential splicing suggests different modes of short-term splicing regulation

Hande Topa*, Antti Honkela

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)
124 Downloads (Pure)

Abstract

Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal physiological functions but also linked to the development of diseases such as cancer. We analyse differential expression and splicing using RNA-sequencing time series in three different settings: overall gene expression levels, absolute transcript expression levels and relative transcript expression levels. Results: Using estrogen receptor α signaling response as a model system, our Gaussian process-based test identifies genes with differential splicing and/or differentially expressed transcripts. We discover genes with consistent changes in alternative splicing independent of changes in absolute expression and genes where some transcripts change whereas others stay constant in absolute level. The results suggest classes of genes with different modes of alternative splicing regulation during the experiment.

Original languageEnglish
Pages (from-to)i147-i155
JournalBioinformatics
Volume32
Issue number12
DOIs
Publication statusPublished - 15 Jun 2016
MoE publication typeA1 Journal article-refereed

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