{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:21Z","timestamp":1740185121572,"version":"3.37.3"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,6,28]],"date-time":"2017-06-28T00:00:00Z","timestamp":1498608000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/F005806\/1","BB\/K003097\/1"],"award-info":[{"award-number":["BB\/F005806\/1","BB\/K003097\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/C544587\/1"],"award-info":[{"award-number":["EP\/C544587\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011102","name":"European Union Seventh Framework Programme","doi-asserted-by":"publisher","award":["FP7\/2007-2013"],"award-info":[{"award-number":["FP7\/2007-2013"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The availability of more data of dynamic gene expression under multiple experimental conditions provides new information that makes the key goal of identifying not only the transcriptional regulators of a gene but also the underlying logical structure attainable.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose a novel method for inferring transcriptional regulation using a simple, yet biologically interpretable, model to find the logic by which a set of candidate genes and their associated transcription factors (TFs) regulate the transcriptional process of a gene of interest. Our dynamic model links the mRNA transcription rate of the target gene to the activation states of the TFs assuming that these interactions are consistent across multiple experiments and over time. A trans-dimensional Markov Chain Monte Carlo (MCMC) algorithm is used to efficiently sample the regulatory logic under different combinations of parents and rank the estimated models by their posterior probabilities. We demonstrate and compare our methodology with other methods using simulation examples and apply it to a study of transcriptional regulation of selected target genes of Arabidopsis Thaliana from microarray time series data obtained under multiple biotic stresses. We show that our method is able to detect complex regulatory interactions that are consistent under multiple experimental conditions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Programs are written in MATLAB and Statistics Toolbox Release 2016b, The MathWorks, Inc., Natick, Massachusetts, United States and are available on GitHub https:\/\/github.com\/giorgosminas\/TRS and at http:\/\/www2.warwick.ac.uk\/fac\/sci\/systemsbiology\/research\/software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx407","type":"journal-article","created":{"date-parts":[[2017,6,27]],"date-time":"2017-06-27T11:10:27Z","timestamp":1498561827000},"page":"3437-3444","source":"Crossref","is-referenced-by-count":0,"title":["Inferring transcriptional logic from multiple dynamic experiments"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7953-706X","authenticated-orcid":false,"given":"Giorgos","family":"Minas","sequence":"first","affiliation":[{"name":"Mathematics Institute, University of Warwick, Coventry, CV4\u20097AL, UK"},{"name":"Zeeman Institute, Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4\u20097AL, UK"}]},{"given":"Dafyd J","family":"Jenkins","sequence":"additional","affiliation":[{"name":"Zeeman Institute, Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4\u20097AL, UK"}]},{"given":"David A","family":"Rand","sequence":"additional","affiliation":[{"name":"Mathematics Institute, University of Warwick, Coventry, CV4\u20097AL, UK"},{"name":"Zeeman Institute, Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4\u20097AL, UK"}]},{"given":"B\u00e4rbel","family":"Finkenst\u00e4dt","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Warwick, Coventry, CV4\u20097AL, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,6,28]]},"reference":[{"volume-title":"An Introduction to Systems Biology: design Principles of Biological Circuits","year":"2014","author":"Alon","key":"2023051506345587600_btx407-B1"},{"key":"2023051506345587600_btx407-B3","doi-asserted-by":"crossref","first-page":"S85","DOI":"10.1098\/rsif.2008.0132.focus","article-title":"Boolean network models of cellular regulation: prospects and limitations","volume":"5","author":"Bornholdt","year":"2008","journal-title":"J. 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