JSM 2005 - Toronto

Abstract #302301

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Activity Number: 42
Type: Invited
Date/Time: Sunday, August 7, 2005 : 4:00 PM to 5:50 PM
Sponsor: Biometrics Section
Abstract - #302301
Title: Identifying Chromosome Clusters and Over-represented Functions of Differentially Expressed Genes in Complementary cDNA Microarray Experiments
Author(s): Erin Conlon*+ and Patrick Eichenberger and Jun S. Liu
Companies: University of Massachusetts and Harvard University and Harvard University
Address: Department of Mathematics and Statistics, Amherst, MA, 01003,
Keywords: Bayesian models ; cDNA microarrays ; functional category ; gene location cluster ; MCMC ; scan statistics
Abstract:

In this paper, we present a Bayesian hierarchical model for determining differentially expressed genes in two complementary replicated cDNA microarray experimental designs. We first normalize the microarray data using a rank invariant method. Genes found to be overexpressed in both experimental designs are further examined for chromosome location and gene function. A global clustering test indicates whether the differentially expressed genes are nonuniformly distributed on the genome. We identify the chromosome locations of clusters of differentially expressed genes using a nearest neighbor scan-statistic. A hypergeometric distribution is used to determine functional categories that are over-represented in subsets of genes, including overexpressed genes and genes with highest and lowest variance in expression. We illustrate our methods using complementary experimental designs in Bacillus subtilis. The first design involves the mutation of a transcription factor, and the second is an overexpression of this factor.

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Revised March 2005