A Bayesian Graphical Model for ChIP-Seq Data on Histone Modifications

REFERENCES

• Andersson , R. , Enroth , S. , Rada-Iglesias , A. , Wadelius , C. and Komorowski , J. 2009 . “Nucleosomes are Well Positioned in Exons and Carry Characteristic Histone Modifications,” . Genome Research , 19 : 1732 – 1741 .
   PubMed Web of Science ®Google Scholar
• Atchade , Y. , Lartillot , N. and Robert , C. 2008 . “Bayesian Computation for Statistical Models With Intractable Normalizing Constants,” . Technical Report, University of Michigan, Department of Statistics
   Google Scholar
• Barbieri , M. and Berger , J. 2004 . “Optimal Predictive Model Selection,” . The Annals of Statistics , 32 : 870 – 897 .
   Web of Science ®Google Scholar
• Barski , A. , Cuddapah , S. , Cui , K. , Roh , T. Y. , Schones , D. E. , Wang , Z. , Wei , G. , Chepelev , I. and Zhao , K. 2007 . “High-Resolution Profiling of Histone Methylations in the Human Genome,” . Cell , 129 : 823 – 837 .
   PubMed Web of Science ®Google Scholar
• Bártfai , R. , Hoeijmakers , W. A. M. , Salcedo-Amaya , A. M. , Smits , A. H. , Janssen-Megens , E. , Kaan , A. , Treeck , M. , Gilberger , T.-W. , Françoijs , K.-J. and Stunnenberg , H. G. 2010 . “H2a.z Demarcates Intergenic Regions of the Plasmodium Falciparum Epigenome That are Dynamically Marked by h3k9ac and h3k4me3,” . PLoS Pathogens , 6 : e1001223
   PubMed Web of Science ®Google Scholar
• Berger , S. 2007 . The Complex Language of Chromatin Regulation During Transcription . Nature , 447 : 407 – 412 .
   PubMed Web of Science ®Google Scholar
• Bergink , S. , Salomons , F. A. , Hoogstraten , D. , Groothuis , T. A. , de Waard , H. , Wu , J. , Yuan , L. , Citterio , E. , Houtsmuller , A. B. , Neefjes , J. , Hoeijmakers , J. H. , Vermeulen , W. and Dantuma , N. P. 2006 . “DNA Damage Triggers Nucleotide Excision Repair-Dependent Monoubiquitylation of Histone H2A,” . Genes and Development , 20 : 1343 – 1352 .
   PubMed Web of Science ®Google Scholar
• Bernstein , B. E. , Humphrey , E. L. , Erlich , R. L. , Schneider , R. , Bouman , P. , Liu , J. S. , Kouzarides , T. and Schreiber , S. L. 2002 . “Methylation of Histone H3 Lys 4 in Coding Regions of Active Genes,” . Proceedings of the National Academy of Science of the United States of America , 99 : 8695 – 8700 .
   PubMed Web of Science ®Google Scholar
• Besag , J. 1974 . “Spatial Interaction and the Statistical Analysis of Lattice Systems,” . Journal of Royal Statistical Society, Series B , 135 : 192 – 236 .
   Google Scholar
• Caragea , C. and Kaiser , S. 2009 . “Autologistic Models With Interpretable Parameters,” . Journal of Agricultural, Biological, and Environmental Statistics , 14 : 281 – 300 .
   Web of Science ®Google Scholar
• Chen , M.-H. and Shao , Q.-M. 1997 . “On Monte Carlo Methods for Estimating Ratios of Normalizing Constants,” . The Annals of Statistics , 25 : 1563 – 1594 .
   Web of Science ®Google Scholar
• Chen , M.-H. , Shao , Q.-M. and Ibrahim , J. 2000 . Monte Carlo Methods in Bayesian Computation , New York : Springer-Verlag .
   Google Scholar
• Ellis , B. and Wong , W. H. 2008 . “Learning Causal Bayesian Network Structures From Experimental Data,” . Journal of the American Statistical Association , 103 : 778 – 789 .
   Web of Science ®Google Scholar
• Friedman , J. , Hastie , T. and Tibshirani , R. 2008 . “Sparse Inverse Covariance Estimation With the Graphical Lasso,” . Biostatistics , 9 : 432 – 441 .
   PubMed Web of Science ®Google Scholar
• Geweke , J. 1991 . “Evaluating the Accuracy of Sampling-Based Approaches to the Calculation of Posterior Momentsin,” . In Bayesian Statistics (Vol. 4) , Edited by: Bernardo , J. M. , Berger , J. , Dawid , A. P. and Smith , A. F. M. 169 – 193 . Oxford : Oxford University Press .
   Google Scholar
• Grant , P. A. and Berger , S. L. 1999 . “Histone Acetyltransferase Complexes,” . Seminars in Cell and Developmental Biology , 10 : 169 – 177 .
   PubMed Web of Science ®Google Scholar
• Green , R. 1995 . “Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination,” . Biometrika , 82 : 711 – 732 .
   Web of Science ®Google Scholar
• Heintzman , N. D. , Hon , G. C. , Hawkins , R. D. , Kheradpour , P. , Stark , A. , Harp , L. F. , Ye , Z. , Lee , L. K. , Stuart , R. K. , Ching , C. W. , Ching , K. A. , Antosiewicz-Bourget , J. E. , Liu , H. , Zhang , X. , Green , R. D. , Lobanenkov , V. V. , Stewart , R. , Thomson , J. A. , Crawford , G. E. , Kellis , M. and Ren , B. 2009 . “Histone Modifications at Human Enhancers Reflect Global Cell-Type-Specific Gene Expression,” . Nature , 459 : 108 – 112 .
   PubMed Web of Science ®Google Scholar
• Hughes , J. , Haran , M. and Caragea , P. 2011 . Autologistic Models for Binary Data on a Lattice . Environmetrics , 22 : 857 – 871 .
   Web of Science ®Google Scholar
• Jones , B. , Carvalho , C. , Dobra , A. , Hans , C. , Carter , C. and West , M. 2004 . “Experiments in Stochastic Computation for High-Dimensional Graphical Models,” . Statistical Science , 20 : 388 – 400 .
   Google Scholar
• Kalisch , M. and Bühlmann , P. 2007 . “Estimating High-Dimensional Directed Acyclic Graphs With the pc-algorithm,” . The Journal of Machine Learning Research , 8 : 613 – 636 .
   Web of Science ®Google Scholar
• Karlić , R. , Chung , H.-R. , Lasserre , J. , Vlahovicek , K. and Vingron , M. 2010 . “Histone Modification Levels are Predictive for Gene Expression,” . Proceedings of the National Academy of Science of the United States of America , 107 : 2926 – 2931 .
   PubMed Web of Science ®Google Scholar
• Kim , T. H. , Barrera , L. O. , Zheng , M. , Qu , C. , Singer , M. A. , Richmond , T. A. , Wu , Y. , Green , R. D. and Ren , B. 2005 . “A High-Resolution Map of Active Promoters in the Human Genome,” . Nature , 436 : 876 – 880 .
   PubMed Web of Science ®Google Scholar
• Kuan , P. , Chung , D. , Pan , G. , Thomson , J. , Stewart , R. and Keles , S. 2009 . “A Hierarchical Semi-Markov Model for Detecting Enrichment With Application to ChIP-Seq Experiments,” . Technical Report 1151, University of Wisconsin
   Google Scholar
• Kuan , P. , Chung , D. , Pan , G. , Thomson , J. , Stewart , R. and Keleş , S. 2011 . A Statistical Framework for the Analysis of Chip-seq Data . Journal of the American Statistical Association , 106 : 891 – 903 .
   PubMed Web of Science ®Google Scholar
• Liu , C. L. , Kaplan , T. , Kim , M. , Buratowski , S. , Schreiber , S. L. , Friedman , N. and Rando , O. J. 2005 . “Single-Nucleosome Mapping of Histone Modifications in S. Cerevisiae,” . PLoS Biology , 3 : e328
   PubMed Web of Science ®Google Scholar
• Marks , P. , Rifkind , R. A. , Richon , V. M. , Breslow , R. , Miller , T. and Kelly , W. K. 2001 . Histone Deacetylases and Cancer: Causes and Therapies . Nature Reviews Cancer , 1 : 194 – 202 .
   PubMed Web of Science ®Google Scholar
• Parmigiani , G. , Garrett , S. , Anbazhagan , R. and Gabrielson , E. 2002 . “A Statistical Framework for Expression-Based Molecular Classification in Cancer,” . Journal of Royal Statistical Society, Series B , 64 : 717 – 736 .
   Google Scholar
• Pokholok , D. K. , Harbison , C. T. , Levine , S. , Cole , M. , Hannett , N. M. , Lee , T. I. , Bell , G. W. , Walker , K. , Rolfe , P. A. , Herbolsheimer , E. , Zeitlinger , J. , Lewitter , F. , Gifford , D. K. and Young , R. A. 2005 . “Genome-Wide Map of Nucleosome Acetylation and Methylation in Yeast,” . Cell , 122 : 517 – 527 .
   PubMed Web of Science ®Google Scholar
• Roh , T. Y. , Cuddapah , S. and Zhao , K. 2005 . “Active Chromatin Domains are Defined by Acetylation Islands Revealed by Genome-Wide Mapping,” . Genes and Development , 19 : 542 – 552 .
   PubMed Web of Science ®Google Scholar
• Rosenfeld , J. , Wang , Z. , Schones , D. , Zhao , K. , DeSalle , R. and Zhang , M. 2009 . “Determination of Enriched Histone Modifications in Non-Genic Portions of the Human Genome,” . BMC Genomics , 10 : 143
   PubMed Web of Science ®Google Scholar
• Rozowsky , J. , Euskirchen , G. , Auerbach , R. , Zhang , D. , Gibson , T. , Bjornson , R. , Carriero , N. , Snyder , M. and Gerstein , M. 2009 . “PeakSeq Enables Systematic Scoring of ChIP-Seq Experiments Relative to Controls,” . Nature Biotechnology , 27 : 66 – 75 .
   PubMed Web of Science ®Google Scholar
• Strahl , B. D. and Allis , C. D. 2000 . “The Language of Covalent Histone Modifications,” . Nature , 403 : 41 – 45 .
   PubMed Web of Science ®Google Scholar
• Su , R.-C. , Brown , K. E. , Saaber , S. , Fisher , A. G. , Merkenschlager , M. and Smale , S. T. 2004 . “Dynamic Assembly of Silent Chromatin During Thymocyte Maturation,” . Nature Genetics , 36 : 502 – 506 .
   PubMedGoogle Scholar
• Telesca , D. , Müller , P. , Kornblau , S. M. , Suchard , M. A. and Ji , Y. 2012 . Modeling Protein Expression and Protein Signaling Pathways . Journal of the American Statistical Association , 107 : 1372 – 1384 .
   Web of Science ®Google Scholar
• Wang , Z. , Zang , C. , Rosenfeld , J. A. , Schones , D. E. , Barski , A. , Cuddapah , S. , Cui , K. , Roh , T. Y. , Peng , W. , Zhang , M. Q. and Zhao , K. 2008 . “Combinatorial Patterns of Histone Acetylations and Methylations in the Human Genome,” . Nature Genetics , 40 : 897 – 903 .
   PubMed Web of Science ®Google Scholar
• Welsh , D. J. A. 1990 . “The Computational Complexity of Some Classical Problems From Statistical Physics,” . In Disorder in Physical Systems , Edited by: Grimmett , G. and Welsh , D. 307 – 321 . Oxford, UK: Clarendon Press .
   Google Scholar
• Zang , C. , Schones , D. E. , Zeng , C. , Cui , K. , Zhao , K. and Peng , W. 2009 . “A Clustering Approach for Identification of Enriched Domains From Histone Modification ChIP-Seq Data,” . Bioinformatics , 25 : 1952 – 1958 .
   PubMed Web of Science ®Google Scholar
• Zhang , Y. , Lv , J. , Liu , H. , Zhu , J. , Su , J. , Wu , Q. , Qi , Y. , Wang , F. and Li , X. 2010 . “HHMD: The Human Histone Modification Database,” . Nucleic Acids Research , 38 : D149 – D154 .
   PubMed Web of Science ®Google Scholar