{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T05:51:55Z","timestamp":1767851515502,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets.<\/jats:p><jats:p>Results: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs.<\/jats:p><jats:p>Availability: If interested in the code for the work presented in this article, please contact the authors.<\/jats:p><jats:p>Contact: \u00a0d.l.wild@warwick.ac.uk<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq210","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i158-i167","source":"Crossref","is-referenced-by-count":60,"title":["Discovering transcriptional modules by Bayesian data integration"],"prefix":"10.1093","volume":"26","author":[{"given":"Richard S.","family":"Savage","sequence":"first","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, 2 Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, 3 School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK and 4 4035 Utah St, San Diego, CA 92104,USA"}]},{"given":"Zoubin","family":"Ghahramani","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, 2 Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, 3 School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK and 4 4035 Utah St, San Diego, CA 92104,USA"}]},{"given":"Jim E.","family":"Griffin","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, 2 Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, 3 School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK and 4 4035 Utah St, San Diego, CA 92104,USA"}]},{"given":"Bernard J.","family":"de la Cruz","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, 2 Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, 3 School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK and 4 4035 Utah St, San Diego, CA 92104,USA"}]},{"given":"David L.","family":"Wild","sequence":"additional","affiliation":[{"name":"1 Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, 2 Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, 3 School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK and 4 4035 Utah St, San Diego, CA 92104,USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508050323100_B1","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1214\/aos\/1176342871","article-title":"Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems","volume":"2","author":"Antoniak","year":"1974","journal-title":"Ann. 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