{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T23:36:41Z","timestamp":1722728201311},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Limited cohort of transcription factors is capable to structure various gene-expression patterns. Transcriptional cooperativity (TC) is deemed to be the main mechanism of complexity and precision in regulatory programs. Although many data types generated from numerous experimental technologies are utilized in an attempt to understand combinational transcriptional regulation, complementary computational approach that can integrate diverse data resources and assimilate them into biological model is still under development.<\/jats:p>\n               <jats:p>Results: We developed a novel Bayesian approach for integrative analysis of proteomic, transcriptomic and genomic data to identify specific TC. The model evaluation demonstrated distinguishable power of features derived from distinct data sources and their essentiality to model performance. Our model outperformed other classifiers and alternative methods. The application that contextualized TC within hepatocarcinogenesis revealed carcinoma associated alterations. Derived TC networks were highly significant in capturing validated cooperativity as well as revealing novel ones. Our methodology is the first multiple data integration approach to predict dynamic nature of TC. It is promising in identifying tissue- or disease-specific TC and can further facilitate the interpretation of underlying mechanisms for various physiological conditions.<\/jats:p>\n               <jats:p>Contact: \u00a0tieliushi01@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt596","type":"journal-article","created":{"date-parts":[[2013,11,6]],"date-time":"2013-11-06T01:50:24Z","timestamp":1383702624000},"page":"823-830","source":"Crossref","is-referenced-by-count":7,"title":["Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach"],"prefix":"10.1093","volume":"30","author":[{"given":"Pengzhan","family":"Hu","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Zhongchao","family":"Shen","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Haibo","family":"Tu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]},{"given":"Tieliu","family":"Shi","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China"}]}],"member":"286","published-online":{"date-parts":[[2013,11,5]]},"reference":[{"key":"2023012710442889300_btt596-B1","doi-asserted-by":"crossref","first-page":"D960","DOI":"10.1093\/nar\/gkq910","article-title":"CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge","volume":"39","author":"Ahmed","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B2","doi-asserted-by":"crossref","first-page":"7024","DOI":"10.1093\/nar\/gkg894","article-title":"Identifying cooperativity among transcription factors controlling the cell cycle in yeast","volume":"31","author":"Banerjee","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B3","doi-asserted-by":"crossref","first-page":"4758","DOI":"10.1002\/j.1460-2075.1995.tb00157.x","article-title":"Cbp-induced stimulation of C-Fos activity is abrogated by E1a","volume":"14","author":"Bannister","year":"1995","journal-title":"Embo. J."},{"key":"2023012710442889300_btt596-B4","doi-asserted-by":"crossref","first-page":"5093","DOI":"10.1038\/sj.onc.1206557","article-title":"Molecular viral oncology of hepatocellular carcinoma","volume":"22","author":"Block","year":"2003","journal-title":"Oncogene"},{"key":"2023012710442889300_btt596-B5","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.cell.2006.06.049","article-title":"Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network","volume":"126","author":"Bookout","year":"2006","journal-title":"Cell"},{"key":"2023012710442889300_btt596-B6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/1471-2164-13-405","article-title":"HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions","volume":"13","author":"Bovolenta","year":"2012","journal-title":"BMC Genomics"},{"key":"2023012710442889300_btt596-B7","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/nrm3118","article-title":"Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis","volume":"12","author":"Braun","year":"2011","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023012710442889300_btt596-B8","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/1471-2105-5-95","article-title":"Clustering proteins from interaction networks for the prediction of cellular functions","volume":"5","author":"Brun","year":"2004","journal-title":"BMC Bioinform."},{"key":"2023012710442889300_btt596-B9","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B10","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1053\/jhep.2002.32524","article-title":"Hypoxia-induced VEGF and collagen I expressions are associated with angiogenesis and fibrogenesis in experimental cirrhosis","volume":"35","author":"Corpechot","year":"2002","journal-title":"Hepatology"},{"key":"2023012710442889300_btt596-B11","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1007\/s11427-010-0096-2","article-title":"Regulation of embryonic stem cell self-renewal and differentiation by TGF-beta family signaling","volume":"53","author":"Fei","year":"2010","journal-title":"Sci. China Life Sci."},{"key":"2023012710442889300_btt596-B12","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.jhep.2008.12.011","article-title":"Angiogenesis in liver disease","volume":"50","author":"Fernandez","year":"2009","journal-title":"J. Hepatol."},{"key":"2023012710442889300_btt596-B13","doi-asserted-by":"crossref","first-page":"12624","DOI":"10.1016\/S0021-9258(18)31434-0","article-title":"Characterization of a novel dentin matrix acidic phosphoprotein. Implications for induction of biomineralization","volume":"268","author":"George","year":"1993","journal-title":"J. Biol. Chem."},{"key":"2023012710442889300_btt596-B14","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from ENCODE data","volume":"489","author":"Gerstein","year":"2012","journal-title":"Nature"},{"key":"2023012710442889300_btt596-B15","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1126\/science.1218370","article-title":"Wnt\/beta-catenin signaling regulates telomerase in stem cells and cancer cells","volume":"336","author":"Hoffmeyer","year":"2012","journal-title":"Science"},{"key":"2023012710442889300_btt596-B16","doi-asserted-by":"crossref","first-page":"D137","DOI":"10.1093\/nar\/gkl1041","article-title":"TRED: a transcriptional regulatory element database, new entries and other development","volume":"35","author":"Jiang","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B17","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/j.cell.2008.02.039","article-title":"An extended transcriptional network for pluripotency of embryonic stem cells","volume":"132","author":"Kim","year":"2008","journal-title":"Cell"},{"key":"2023012710442889300_btt596-B18","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.tig.2012.03.006","article-title":"Mechanisms of transcriptional precision in animal development","volume":"28","author":"Lagha","year":"2012","journal-title":"Trends Genet."},{"key":"2023012710442889300_btt596-B19","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1016\/S1357-2725(97)00085-X","article-title":"Transcription factors: an overview","volume":"29","author":"Latchman","year":"1997","journal-title":"Int. J. Biochem. Cell B"},{"key":"2023012710442889300_btt596-B20","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1101\/gad.831000","article-title":"Orchestrated response: a symphony of transcription factors for gene control","volume":"14","author":"Lemon","year":"2000","journal-title":"Gene Dev."},{"key":"2023012710442889300_btt596-B21","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1038\/nature02782","article-title":"Genomic analysis of regulatory network dynamics reveals large topological changes","volume":"431","author":"Luscombe","year":"2004","journal-title":"Nature"},{"key":"2023012710442889300_btt596-B22","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/msb.2008.55","article-title":"InnateDB: facilitating systems-level analyses of the mammalian innate immune response","volume":"4","author":"Lynn","year":"2008","journal-title":"Mol. Syst. Biol."},{"key":"2023012710442889300_btt596-B23","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B24","doi-asserted-by":"crossref","first-page":"e9289","DOI":"10.1371\/journal.pone.0009289","article-title":"A comprehensive resource of interacting protein regions for refining human transcription factor networks","volume":"5","author":"Miyamoto-Sato","year":"2010","journal-title":"PLoS One"},{"key":"2023012710442889300_btt596-B25","doi-asserted-by":"crossref","first-page":"4828","DOI":"10.1093\/nar\/gki793","article-title":"Identifying cooperative transcriptional regulations using protein-protein interactions","volume":"33","author":"Nagamine","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B26","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1080\/03008200290000592","article-title":"Transcriptional regulation of dentin matrix protein 1 (DMP1) by AP-1 (c-fos\/c-jun) factors","volume":"43","author":"Narayanan","year":"2002","journal-title":"Connect Tissue Res."},{"key":"2023012710442889300_btt596-B27","doi-asserted-by":"crossref","first-page":"44294","DOI":"10.1074\/jbc.M403511200","article-title":"Transcriptional regulation of dentin matrix protein 1 by JunB and p300 during osteoblast differentiation","volume":"279","author":"Narayanan","year":"2004","journal-title":"J. Biol. Chem."},{"key":"2023012710442889300_btt596-B28","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.cell.2012.04.040","article-title":"Circuitry and dynamics of human transcription factor regulatory networks","volume":"150","author":"Neph","year":"2012","journal-title":"Cell"},{"key":"2023012710442889300_btt596-B29","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1158\/1055-9965.EPI-12-1169","article-title":"Alcohol consumption, folate intake, hepatocellular carcinoma incidence and liver disease mortality","volume":"22","author":"Persson","year":"2013","journal-title":"Cancer Epidemiol. Biomarkers. Prev."},{"key":"2023012710442889300_btt596-B30","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/ng724","article-title":"Identifying regulatory networks by combinatorial analysis of promoter elements","volume":"29","author":"Pilpel","year":"2001","journal-title":"Nat. Genet."},{"key":"2023012710442889300_btt596-B31","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1182\/blood-2010-08-298810","article-title":"Dentin matrix protein 1 induces membrane expression of VE-cadherin on endothelial cells and inhibits VEGF-induced angiogenesis by blocking VEGFR-2 phosphorylation","volume":"117","author":"Pirotte","year":"2011","journal-title":"Blood"},{"key":"2023012710442889300_btt596-B32","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","article-title":"Human protein reference database-2009 update","volume":"37","author":"Prasad","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B33","doi-asserted-by":"crossref","first-page":"D497","DOI":"10.1093\/nar\/gkp914","article-title":"CORUM: the comprehensive resource of mammalian protein complexes\u20142009","volume":"38","author":"Ruepp","year":"2010","journal-title":"Nucleic Acids. Res."},{"key":"2023012710442889300_btt596-B34","doi-asserted-by":"crossref","first-page":"D106","DOI":"10.1093\/nar\/gkq945","article-title":"TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins","volume":"39","author":"Schaefer","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B35","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1007\/s00774-004-0504-4","article-title":"Expression of dentin matrix protein 1 (DMP1) in nonmineralized tissues","volume":"22","author":"Terasawa","year":"2004","journal-title":"J. Bone Miner. Metab."},{"key":"2023012710442889300_btt596-B36","doi-asserted-by":"crossref","first-page":"2845","DOI":"10.1038\/sj.onc.1201125","article-title":"ETS1, NFkappaB and AP1 synergistically transactivate the human GM-CSF promoter","volume":"14","author":"Thomas","year":"1997","journal-title":"Oncogene"},{"key":"2023012710442889300_btt596-B37","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1101\/gr.139105.112","article-title":"Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors","volume":"22","author":"Wang","year":"2012","journal-title":"Genome Res."},{"key":"2023012710442889300_btt596-B38","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1073\/pnas.0405537102","article-title":"Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation","volume":"102","author":"Wang","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710442889300_btt596-B39","doi-asserted-by":"crossref","first-page":"5943","DOI":"10.1093\/nar\/gkp625","article-title":"Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data","volume":"37","author":"Wang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B40","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1091\/mbc.02-02-0030","article-title":"Identification of genes periodically expressed in the human cell cycle and their expression in tumors","volume":"13","author":"Whitfield","year":"2002","journal-title":"Mol. Biol. Cell"},{"key":"2023012710442889300_btt596-B41","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2012-13-9-r50","article-title":"Functional analysis of transcription factor binding sites in human promoters","volume":"13","author":"Whitfield","year":"2012","journal-title":"Genome Biol."},{"key":"2023012710442889300_btt596-B42","doi-asserted-by":"crossref","first-page":"3602","DOI":"10.1073\/pnas.91.9.3602","article-title":"p53 and E2F-1 cooperate to mediate apoptosis","volume":"91","author":"Wu","year":"1994","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710442889300_btt596-B43","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/S0168-9525(03)00175-6","article-title":"Genomic analysis of gene expression relationships in transcriptional regulatory networks","volume":"19","author":"Yu","year":"2003","journal-title":"Trends Genet."},{"key":"2023012710442889300_btt596-B44","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1093\/nar\/gkj487","article-title":"Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae","volume":"34","author":"Yu","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B45","doi-asserted-by":"crossref","first-page":"4925","DOI":"10.1093\/nar\/gkl595","article-title":"Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues","volume":"34","author":"Yu","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012710442889300_btt596-B46","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1007\/s11427-012-4384-x","article-title":"The role and clinical implications of microRNAs in hepatocellular carcinoma","volume":"55","author":"Zhao","year":"2012","journal-title":"Sci. China Life Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/6\/823\/48920091\/bioinformatics_30_6_823.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/6\/823\/48920091\/bioinformatics_30_6_823.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:08:13Z","timestamp":1674817693000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/6\/823\/285467"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,5]]},"references-count":46,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2014,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt596","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,3,15]]},"published":{"date-parts":[[2013,11,5]]}}}