{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T09:12:04Z","timestamp":1715073124062},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1301,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription\u2013polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states.<\/jats:p><jats:p>Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation.<\/jats:p><jats:p>Contact: \u00a0B.F.Finkenstadt@Warwick.ac.uk<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt111","type":"journal-article","created":{"date-parts":[[2013,3,12]],"date-time":"2013-03-12T02:23:45Z","timestamp":1363055025000},"page":"1158-1165","source":"Crossref","is-referenced-by-count":14,"title":["A temporal switch model for estimating transcriptional activity in gene expression"],"prefix":"10.1093","volume":"29","author":[{"given":"Dafyd J.","family":"Jenkins","sequence":"first","affiliation":[{"name":"1 Warwick Systems Biology Centre and 2Department of Statistics, University of Warwick, Coventry CV4 7AL, UK"}]},{"given":"B\u00e4rbel","family":"Finkenst\u00e4dt","sequence":"additional","affiliation":[{"name":"1 Warwick Systems Biology Centre and 2Department of Statistics, University of Warwick, Coventry CV4 7AL, UK"}]},{"given":"David A.","family":"Rand","sequence":"additional","affiliation":[{"name":"1 Warwick Systems Biology Centre and 2Department of Statistics, University of Warwick, Coventry CV4 7AL, UK"}]}],"member":"286","published-online":{"date-parts":[[2013,3,11]]},"reference":[{"key":"2023012810404447800_btt111-B1","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/s00285-007-0115-5","article-title":"Semi-algebraic optimization of temperature compensation in a general switch-type negative feedback model of circadian clocks","volume":"56","author":"Aase","year":"2008","journal-title":"J. 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