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

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dc.contributor University of Helsinki, Helsinki Institute for Information Technology en
dc.contributor University of Helsinki, Helsinki Institute for Information Technology en
dc.contributor.author Topa, Hande
dc.contributor.author Honkela, Antti
dc.date.accessioned 2017-10-04T07:07:01Z
dc.date.available 2017-10-04T07:07:01Z
dc.date.issued 2016-06-15
dc.identifier.citation Topa , H & Honkela , A 2016 , ' Analysis of differential splicing suggests different modes of short-term splicing regulation ' , Bioinformatics , vol. 32 , no. 12 , pp. 147-155 . https://doi.org/10.1093/bioinformatics/btw283 en
dc.identifier.issn 1367-4803
dc.identifier.other PURE: 65041856
dc.identifier.other PURE UUID: c224264b-9649-4129-984e-e1e44adb1935
dc.identifier.other WOS: 000379734300017
dc.identifier.other Scopus: 84976477915
dc.identifier.other ORCID: /0000-0001-9193-8093/work/28762888
dc.identifier.uri http://hdl.handle.net/10138/225051
dc.description.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. AVAILABILITY AND IMPLEMENTATION: R and Matlab codes implementing the method are available at https://github.com/PROBIC/diffsplicing An interactive browser for viewing all model fits is available at http://users.ics.aalto.fi/hande/splicingGP/ en
dc.format.extent 9
dc.language.iso eng
dc.relation.ispartof Bioinformatics
dc.rights en
dc.subject 113 Computer and information sciences en
dc.title Analysis of differential splicing suggests different modes of short-term splicing regulation en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1093/bioinformatics/btw283
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
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