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Motivation: Alternative splicing is an important mechanism in which theregions of pre-mRNAs are differentially joined in order to form differenttranscript isoforms. Alternative splicing is involved in the regulation ofnormal physiological functions but also linked to the development of diseasessuch as cancer. We analyse differential expression and splicing using RNA-seqtime series in three different settings: overall gene expression levels,absolute transcript expression levels and relative transcript expressionlevels.  Results: Using estrogen receptor $\alpha$ signalling response as a modelsystem, our Gaussian process (GP)-based test identifies genes with differentialsplicing and/or differentially expressed transcripts. We discover genes withconsistent changes in alternative splicing independent of changes in absoluteexpression and genes where some transcripts change while others stay constantin absolute level. The results suggest classes of genes with different modes ofalternative splicing regulation during the experiment.  Availability: R and Matlab codes implementing the method are available athttps://github.com/PROBIC/diffsplicing . An interactive browser for viewing allmodel fits is available at http://users.ics.aalto.fi/hande/splicingGP/ .

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