title: CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data.
abstract: 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 'regulome' and the associated gene expression programs.
  
  
  
  http://bioinfo.icts.hkbu.edu.hk/cmgrn; http://www.byanbioinfo.org/cmgrn CONTACT: yanbinai6017@gmail.com or junwen@hku.hk Supplementary Information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Daogang
authors.initials: D
authors.lastname: Guan
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Jiaofang
authors.initials: J
authors.lastname: Shao
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Youping
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Panwen
authors.initials: P
authors.lastname: Wang
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Zhongying
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China Department of Biology, Hong Kong Baptist University, Hong Kong, China, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA, Department of Biochemistry and HKU-SIRI, Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China and Key Laboratory of Acupuncture and Medicine Research of Minister of Education , Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yan
mesh_terms: D001499:Bayes Theorem; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D003195:Computer Communication Networks; D044127:Epigenesis, Genetic; D015870:Gene Expression; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors