title: Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies.
abstract: Hidden Markov model (HMM) is widely used for modeling spatially correlated genomic data (series data). In genomics, datasets of this kind are generated from genome-wide mapping studies through high-throughput methods such as chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq). When multiple regulatory protein binding sites or related epigenetic modifications are mapped simultaneously, the correlation between data series can be incorporated into the latent variable inference in a multivariate form of HMM, potentially increasing the statistical power of signal detection. In this chapter, we review the challenges of multivariate HMMs and propose a computationally tractable method called sparsely correlated HMMs (scHMM). We illustrate the method and the scHMM package using an example mouse ChIP-seq dataset.
authors.affiliation: Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore, 117549, Singapore. hyung_won_choi@nuhs.edu.sg.
authors.forename: Hyungwon
authors.initials: H
authors.lastname: Choi
authors.affiliation: Department of Biostatstics & Informatics, University of Colorado Anschutz Medical Campus, University Park, State College, PA, USA.
authors.forename: Debashis
authors.initials: D
authors.lastname: Ghosh
authors.affiliation: Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA.|Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA.
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Qin
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D044127:Epigenesis, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D051379:Mice; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: Genome-wide mapping study; Hidden Markov model