{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T15:56:06Z","timestamp":1757778966119},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: ChIP-seq technology provides an accurate characterization of transcription or epigenetic factors binding on genomic sequences. With integration of such ChIP-based and other high-throughput information, it would be dedicated to dissecting cross-interactions among multilevel regulators, genes and biological functions. Here, we devised an integrative web server CMGRN (constructing multilevel gene regulatory networks), to unravel hierarchical interactive networks at different regulatory levels. The newly developed method used the Bayesian network modeling to infer causal interrelationships among transcription factors or epigenetic modifications by using ChIP-seq data. Moreover, it used Bayesian hierarchical model with Gibbs sampling to incorporate binding signals of these regulators and gene expression profile together for reconstructing gene regulatory networks. The example applications indicate that CMGRN provides an effective web-based framework that is able to integrate heterogeneous high-throughput data and to reveal hierarchical \u2018regulome\u2019 and the associated gene expression programs.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinfo.icts.hkbu.edu.hk\/cmgrn; http:\/\/www.byanbioinfo.org\/cmgrn.<\/jats:p>\n               <jats:p>Contact: \u00a0yanbinai6017@gmail.com or junwen@hku.hk<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt761","type":"journal-article","created":{"date-parts":[[2014,1,4]],"date-time":"2014-01-04T02:03:14Z","timestamp":1388800994000},"page":"1190-1192","source":"Crossref","is-referenced-by-count":26,"title":["CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data"],"prefix":"10.1093","volume":"30","author":[{"given":"Daogang","family":"Guan","sequence":"first","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Jiaofang","family":"Shao","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Youping","family":"Deng","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Panwen","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Zhongying","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Yan","family":"Liang","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Junwen","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"},{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]},{"given":"Bin","family":"Yan","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"},{"name":"1 Department of Biology, Hong Kong Baptist University, Hong Kong, China, 2Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, 3Department of Biochemistry and HKU-SIRI, 4Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and 5Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China"}]}],"member":"286","published-online":{"date-parts":[[2014,1,2]]},"reference":[{"key":"2023012710490995100_btt761-B1","first-page":"1027","article-title":"kmeans++: the advantages of careful seeding","volume-title":"Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms","author":"Arthur","year":"2007"},{"key":"2023012710490995100_btt761-B2","doi-asserted-by":"crossref","first-page":"R4","DOI":"10.1186\/gb-2007-8-1-r4","article-title":"Clustering of genes into regulons using 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