{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T10:09:14Z","timestamp":1767262154335},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this article we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past research, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the overlap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format.<\/jats:p>\n               <jats:p>Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, Escherichia coli and Human organisms. We also investigate the effect of weighting the influence of the prior knowledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways.<\/jats:p>\n               <jats:p>Contact: \u00a0emma.steele@brunel.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp277","type":"journal-article","created":{"date-parts":[[2009,4,24]],"date-time":"2009-04-24T00:25:34Z","timestamp":1240532734000},"page":"1768-1774","source":"Crossref","is-referenced-by-count":29,"title":["Literature-based priors for gene regulatory networks"],"prefix":"10.1093","volume":"25","author":[{"given":"E.","family":"Steele","sequence":"first","affiliation":[{"name":"1 Centre for Intelligent Data Analysis, School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge UB8 3PH, UK and 2 Biosemantics Association, a collaboration between the Department of Human Genetics from the Leiden University Medical Center, Leiden and Department of Medical Informatics from the Erasmus University Medical Center, Rotterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.","family":"Tucker","sequence":"additional","affiliation":[{"name":"1 Centre for Intelligent Data Analysis, School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge UB8 3PH, UK and 2 Biosemantics Association, a collaboration between the Department of Human Genetics from the Leiden University Medical Center, Leiden and Department of Medical Informatics from the Erasmus University Medical Center, Rotterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P.A.C. 't","family":"Hoen","sequence":"additional","affiliation":[{"name":"1 Centre for Intelligent Data Analysis, School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge UB8 3PH, UK and 2 Biosemantics Association, a collaboration between the Department of Human Genetics from the Leiden University Medical Center, Leiden and Department of Medical Informatics from the Erasmus University Medical Center, Rotterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.J.","family":"Schuemie","sequence":"additional","affiliation":[{"name":"1 Centre for Intelligent Data Analysis, School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge UB8 3PH, UK and 2 Biosemantics Association, a collaboration between the Department of Human Genetics from the Leiden University Medical Center, Leiden and Department of Medical Informatics from the Erasmus University Medical Center, Rotterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,4,23]]},"reference":[{"key":"2023013112050381100_B1","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1210\/mend.13.7.0305","article-title":"The nuclear receptor corepressor n-cor regulates differentiation: N-cor directly interacts with myod","volume":"13","author":"Bailey","year":"1999","journal-title":"Mol. Endocrinol."},{"key":"2023013112050381100_B2","first-page":"459","article-title":"Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data","volume-title":"Proceedings of the Pacific Symposium on Biocomputing 2005","author":"Bernard","year":"2005"},{"key":"2023013112050381100_B3","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0888-613X(99)00041-9","article-title":"Priors on network structures: biasing the search for Bayesian networks","volume":"24","author":"Castelo","year":"2000","journal-title":"Int. J. Approx. Reason."},{"key":"2023013112050381100_B4","article-title":"A transformational characterization of equivalent Bayesian network structures","volume-title":"Proceedings of Uncertainty in Artificial Intelligence","author":"Chickering","year":"1995"},{"key":"2023013112050381100_B5","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/S0301-472X(01)00780-9","article-title":"Modulation of mdm2\/p53 and cyclin-activating kinase during the megakaryocyte differentiation of human erythroleukemia cells","volume":"30","author":"Datta","year":"2002","journal-title":"Exp. Hematol."},{"key":"2023013112050381100_B6","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-4541-9","volume-title":"An Introduction to the Bootstrap.","author":"Efron","year":"1993"},{"key":"2023013112050381100_B7","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1198\/016214506000001211","article-title":"Correlation and large-scale simultaneous significance testing","volume":"102","author":"Efron","year":"2007","journal-title":"J. Am. Stat. Assoc."},{"key":"2023013112050381100_B8","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0050008","article-title":"Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles","volume":"5","author":"Faith","year":"2007","journal-title":"PLoS Biol."},{"key":"2023013112050381100_B9","article-title":"Data analysis with Bayesian networks: a bootstrap approach","volume-title":"Proceedings of 15th Annual Conference on Uncertainty in Artificial Intelligence.","author":"Friedman","year":"1999"},{"key":"2023013112050381100_B10","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian networks to analyze expression data","volume":"7","author":"Friedman","year":"2000","journal-title":"J. Comput. Biol."},{"key":"2023013112050381100_B11","doi-asserted-by":"crossref","DOI":"10.1186\/1752-0509-1-11","article-title":"Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge","volume":"1","author":"Geier","year":"2007","journal-title":"BMC Syst. Biol."},{"key":"2023013112050381100_B12","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1128\/MCB.00882-06","article-title":"Histone deacetylase 3 interacts with and deacetylates myocyte enhancer factor 2","volume":"27","author":"Gregoire","year":"2007","journal-title":"Mol. Cell. Biol."},{"key":"2023013112050381100_B13","first-page":"37","article-title":"Bayesian methods for elucidating genetic regulatory networks","volume":"17","author":"Hartemink","year":"2002","journal-title":"IEEE Intell. Syst."},{"key":"2023013112050381100_B14","first-page":"104","article-title":"Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks","volume-title":"Proceedings of the IEEE Computer Science Bioinformatics Conference (CSB'03) IEEE","author":"Imoto","year":"2003"},{"key":"2023013112050381100_B15","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2105-8-14","article-title":"Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation","volume":"8","author":"Jelier","year":"2007","journal-title":"BMC Bioinform."},{"key":"2023013112050381100_B16","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.ijmedinf.2007.07.004","article-title":"Literature-based concept profiles for gene annotation: The issue of weighting","volume":"77","author":"Jelier","year":"2008","journal-title":"Int. J. Med. Inform."},{"key":"2023013112050381100_B17","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/sj.onc.1201529","article-title":"Interferon-induces expression of cyclin-dependent kinase-inhibitors p21waf1 and p27kip1 that prevent activation of cyclin-dependent kinase by cdk-activating kinase (cak)","volume":"16","author":"Mandalb","year":"1998","journal-title":"Oncogene"},{"key":"2023013112050381100_B18","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nbt1239","article-title":"The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements","volume":"24","author":"MAQC consortium","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023013112050381100_B19","first-page":"484","article-title":"Making the conceptual connections: the Unified Medical Language System (UMLS) after a decade of research and development","volume":"4","author":"McCray","year":"1998","journal-title":"J. Am. Med. Inf. Assoc."},{"key":"2023013112050381100_B20","volume-title":"Handbook of Biological Statistics","author":"McDonald","year":"2008"},{"key":"2023013112050381100_B21","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-373","article-title":"Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine- 1-phosphate and invasiveness of a glioblastoma cell line","volume":"7","author":"Natarajan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013112050381100_B22","volume-title":"Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference","author":"Pearl","year":"1991"},{"key":"2023013112050381100_B23","first-page":"441","article-title":"A theory of inferred causation","volume-title":"Proceedings of Knowledge Representation and Reasoning","author":"Pearl","year":"1991"},{"key":"2023013112050381100_B24","doi-asserted-by":"crossref","first-page":"2266","DOI":"10.1101\/gad.1450606","article-title":"The forkhead transcription factor hcm1 regulates chromosome segregation genes and fills the s-phase gap in the transcriptional circuitry of the cell cycle","volume":"20","author":"Pramila","year":"2006","journal-title":"Genes Dev."},{"key":"2023013112050381100_B25","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/nar\/gkj156","article-title":"Regulondb (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions","volume":"34","author":"Salgado","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023013112050381100_B26","doi-asserted-by":"crossref","first-page":"R32","DOI":"10.1186\/gb-2006-7-4-r32","article-title":"A classification based framework for quantitative description of large-scale microarray data","volume":"7","author":"Sangurdekar","year":"2006","journal-title":"Genome Biol."},{"key":"2023013112050381100_B27","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1002\/pmic.200600693","article-title":"Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE","volume":"7","author":"Schuemie","year":"2007","journal-title":"Proteomics"},{"key":"2023013112050381100_B28","article-title":"Peregrine: lightweight gene name normalization by dictionary lookup","author":"Schuemie","year":"2007","journal-title":"Proceedings of the Biocreative 2 Workshop. Madrid"},{"key":"2023013112050381100_B29","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1145\/565196.565231","article-title":"From promoter sequence to expression: a probabilistic framework","volume-title":"RECOMB '02: Proceedings of the Sixth Annual International Conference on Computational Biology","author":"Segal","year":"2002"},{"key":"2023013112050381100_B30","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1038\/ng1434","article-title":"A module map showing conditional activity of expression modules in cancer","volume":"36","author":"Segal","year":"2004","journal-title":"Nat. Genet."},{"key":"2023013112050381100_B31","first-page":"3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Cell"},{"key":"2023013112050381100_B32","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.nbd.2006.03.004","article-title":"Gene expression profiling highlights defective myogenesis in DMD patients and a possible role for bone morphogenetic protein 4","volume":"23","author":"Sterrenburg","year":"2006","journal-title":"Neurobiol. Dis."},{"key":"2023013112050381100_B33","doi-asserted-by":"crossref","first-page":"5676","DOI":"10.1093\/nar\/gkg763","article-title":"Evaluation of gene expression measurements from commercial microarray platforms","volume":"31","author":"Tan","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023013112050381100_B34","doi-asserted-by":"crossref","first-page":"D446","DOI":"10.1093\/nar\/gkj013","article-title":"The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae","volume":"34","author":"Teixeira","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023013112050381100_B35","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1282","article-title":"Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge","volume":"6","author":"Werhli","year":"2007","journal-title":"Stat. Appl. Genet. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/14\/1768\/48993360\/bioinformatics_25_14_1768.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/14\/1768\/48993360\/bioinformatics_25_14_1768.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:19:47Z","timestamp":1675199987000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/14\/1768\/224246"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,23]]},"references-count":35,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2009,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp277","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,7,15]]},"published":{"date-parts":[[2009,4,23]]}}}