Integrative Analyses for Omics Data: A Bayesian Mixture Model to Assess the Concordance of ChIP-chip and ChIP-seq Measurements

REFERENCES

• Bolstad , B. M. , Irizarry , R. A. , Åstrand , M. and Speed , T. P. 2003 . A comparison of normalization methods for high density oligonucleotide array data based on variance and bias . Bioinformatics , 19 : 185 – 93 .
   PubMed Web of Science ®Google Scholar
• Bröet , P. and Richardson , S. 2006 . Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model . Bioinformatics , 22 : 911 – 18 .
   PubMed Web of Science ®Google Scholar
• Elling , C. , Erben , P. , Walz , C. , Frickenhaus , M. , Schemionek , M. , Stehling , M. , Serve , H. , Cross , N. C. P. , Hochhaus , A. , Hofmann , W.-K. , Berdel , W. E. , Müller-Tidow , C. , Reiter , A. and Koschmieder , S. 2011 . Novel imatinib-sensitive PDGFRA-activating point mutations in hypereosinophilic syndrome induce growth factor independence and leukemia-like disease . Blood , 117 : 2935 – 43 .
   PubMed Web of Science ®Google Scholar
• Gallegos , R. , Mariëlle , I. , Floor , K. , Roepman , P. , Rodriguez , J. A. , Meijer , G. A. , Mooi , W. J. , Jassem , E. , Niklinski , J. , Muley , T. , van Zandwijk , N. , Smit , E. F. , Beebe , K. , Neckers , L. , Ylstra , B. and Giaccone , G. 2008 . Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target . PLoS ONE , 3 : e0001722
   PubMedGoogle Scholar
• Ho , W. K. J. , Bishop , E. , Karchenko , P. V. , Negré , N. , White , K. P. and Park , P. J. 2011 . ChIP-chip versus ChIP-seq. Lessons for experimental design and data analysis . BMC Genomics , 12 : 134
   PubMed Web of Science ®Google Scholar
• Kuan , P. F. , Chung , D. , Pan , G. , Thomson , J. A. , Stewart , R. and Keleş , S. 2011 . A statistical framework for the analysis of ChIP-seq data . J. Am. Stat. Assoc. , 106 : 891 – 903 .
   PubMed Web of Science ®Google Scholar
• Li , H. and Durbin , R. 2009 . Fast and accurate short read alignment with Burrows–Wheeler transform . Bioinformatics , 25 : 1754 – 60 .
   PubMed Web of Science ®Google Scholar
• Mo , Q. and Liang , F. 2010 . Bayesian modeling of ChIP-chip data through a high-order Ising model . Biometrics , 66 : 1284 – 94 .
   PubMed Web of Science ®Google Scholar
• Mockler , T. C. and Ecker , J. R. 2005 . Applications of DNA tiling arrays for whole-genome analysis . Genomics , 85 : 1 – 15 .
   PubMed Web of Science ®Google Scholar
• Ortiz-Estevez , M. , De las Rivas , J. , Fontanillo , C. and Rubio , A. 2011 . Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene–loci expression . Genomics , 97 : 86 – 93 .
   PubMed Web of Science ®Google Scholar
• Park , P. J. 2009 . ChIP-seq: Advantages and challenges of a maturing technology . Nat. Rev. Genet. , 10 : 669 – 80 .
   PubMed Web of Science ®Google Scholar
• R Developent Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria http://www.R-project.org (http://www.R-project.org)
   Google Scholar
• Schäfer , M. , Schwender , H. , Merk , S. , Haferlach , C. , Ickstadt , K. and Dugas , M. 2009 . Integrated analysis of copy number alterations gene expression: a bivariate assessment of equally directed abnormalities . Bioinformatics , 25 : 3228 – 35 .
   PubMed Web of Science ®Google Scholar
• Spiegelhalter, D., Thomas, A., Best, N., Lunn, D. 2003. WinBUGS User Manual, Version 1.4. http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/manual14.pdf (http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/manual14.pdf) (Accessed: 23 August 2011 ).
   Google Scholar
• van Wieringen , W. N. and van de Wiel , M. A. 2009 . Nonparametric testing for DNA copy number induced differential mRNA gene expression . Biometrics , 65 : 19 – 29 .
   PubMed Web of Science ®Google Scholar
• Vega , V. B. , Cheung , E. , Palanisamy , N. and Sung , W.-K. 2009 . Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries . PLoS One , 4 : e5241
   PubMedGoogle Scholar
• Wei , P. and Pan , W. 2008 . Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model . Bioinformatics , 24 : 404 – 11 .
   PubMed Web of Science ®Google Scholar
• Zacher , B. , Kuan , P. F. and Tresch , A. 2010 . Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data . BMC Bioinformatics , 11 : 194 doi: 10.1186/1471-2105-11-194
   PubMed Web of Science ®Google Scholar