Bayesian Inference for Gene Expression and Proteomics

The interdisciplinary nature of bioinformatics presents a challenge in integrating concepts, methods, software, and multi-platform data. Although there have been rapid developments in new technology and an inundation of statistical methodology and software for the analysis of microarray gene expression arrays, there exist few rigorous statistical methods for addressing other types of high-throughput data, such as proteomic profiles that arise from mass spectrometry experiments. This book discusses the development and application of Bayesian methods in the analysis of high-throughput bioinformatics data, from medical research and molecular and structural biology. The Bayesian approach has the advantage that evidence can be easily and flexibly incorporated into statistical models. A basic overview of the biological and technical principles behind multi-platform high-throughput experimentation is followed by expert reviews of Bayesian methodology, tools, and software for single group inference, group comparisons, classification and clustering, motif discovery and regulatory networks, and Bayesian networks and gene interactions.

• Novel Bayesian methods for the analysis of high throughput bioinformatics data
• Applications to translational research
• Special case studies

Contents

1. An introduction to high-throughput bioinformatics data Keith Baggerly, Kevin Coombes and Jeffrey S. Morris; 2. Hierarchical mixture models for expression profiles Michael Newton, Ping Wang and Christina Kendziorski; 3. Bayesian hierarchical models for inference in microarray data Anne-Mette K. Hein, Alex Lewin and Sylvia Richardson; 4. Bayesian process-based modeling of two-channel microarray experiments estimating absolute mRNA concentrations Mark A. van de Wiel, Marit Holden, Ingrid K. Glad, Heidi Lyng and Arnoldo Frigessi; 5. Identification of biomarkers in classification and clustering of high-throughput data Mahlet Tadesse, Marina Vannucci, Naijun Sha and Sinae Kim; 6. Modeling nonlinear gene interactions using Bayesian MARS Veerabhadran Baladandayuthapani Chris C. Holmes, Bani K. Mallick and Raymond J. Carroll; 7. Models for probability of under- and overexpression: the POE scale Elizabeth Garrett-Mayer and Robert Scharpf; 8. Sparse statistical modelling in gene expression genomics Joseph Lucas, Carlos Carvalho, Quanli Wang, Andrea Bild, Joseph Nevins and Mike West; 9. Bayesian analysis of cell-cycle gene expression Chuan Zhou, Jon Wakefield and Linda L. Breeden; 10. Model-based clustering for expression data via a Dirichlet process mixture model David Dahl; 11. Interval mapping for Expression Quantitative Trait Loci mapping Meng Chen and Christina Kendziorski; 12. Bayesian mixture model for gene expression and protein profiles Michele Guindani, Kim-Anh Do, Peter Müller and Jeffrey S. Morris; 13. Shrinkage estimation for SAGE data using a mixture Dirichlet prior Jeffrey S. Morris, Kevin Coombes and Keith Baggerly; 14. Analysis of mass spectrometry data using Bayesian wavelet-based functional mixed models Jeffrey S. Morris, Philip J. Brown, Keith Baggerly and Kevin Coombes; 15. Nonparametric models for proteomic peak identification and quantification Merlise Clyde, Leanna House and Robert Wolpert; 16. Bayesian modeling and inference for sequence motif discovery Mayetri Gupta and Jun S. Liu; 17. Identifying of DNA regulatory motifs and regulators by integrating gene expression and sequence data Deuk Woo Kwon, Sinae Kim, David Dahl, Michael Swartz, Mahlet Tadesse and Marina Vannucci; 18. A misclassification model for inferring transcriptional regulatory networks Ning Sun and Hongyu Zhao; 19. Estimating cellular signaling from transcription data Andrew V. Kossenkov, Ghislain Bidaut and Michael Ochs; 20. Computational methods for learning Bayesian networks from high-throughput biological data Bradley Broom and Devika Subramanian; 21. Modeling transcriptional regulation: Bayesian networks and informative priors Alexander J. Hartemink; 22. Sample size choice for microarray experiments Peter Müller, Christian Robert and Judith Rousseau.

Review

' … an authoritative volume … presents the state of the art statistical techniques that are starting to make an impact at the forefronts of modern scientific discovery.' Journal of the RSS