Statistics Seminar: Dr. Subharup Guha
Speaker: Dr. Subharup Guha, University of Florida
Title: Bayesian Nonparametric Differential Analysis for Dependent Multigroup Data with Application to DNA Methylation Analyses
Cancer 'omics datasets involve widely varying sizes and scales, measurement variables, and correlation structures. An overarching scientific goal in cancer research is the development of general statistical techniques that can cleanly sift the signal from the noise in identifying genomic signatures of the disease across a set of experimental or biological conditions. We propose BayesDiff, a nonparametric Bayesian approach based on a novel class of first order mixture models, called the Sticky Poisson-Dirichlet process or multicuisine restaurant franchise. The BayesDiff methodology flexibly utilizes information from all the measurements and adaptively accommodates any serial dependence in the data, accounting for the inter-probe distances, to perform simultaneous inferences on the variables. The technique is applied to analyze the motivating DNA methylation gastrointestinal cancer dataset, which displays both serial correlations and complex interaction patterns. In simulation studies, we demonstrate the effectiveness of the BayesDiff procedure relative to existing techniques for differential DNA methylation. Returning to the motivating dataset, we detect the genomic signature for four types of upper gastrointestinal cancer. The analysis results support and complement known features of DNA methylation as well as gene association with gastrointestinal cancer.
(joint work with Chiyu Gu of Monsanto Company and Veerabhadran Baladandayuthapani of University of Michigan)
Open to all
Department of Mathematical Sciences