Statistical Framework for Phylogenomic Analysis of Gene Family Expression Profiles

Author:

Gu Xun1

Affiliation:

1. Department of Genetics, Development and Cell Biology (GDCB), Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa 50011

Abstract

Abstract Microarray technology has produced massive expression data that are invaluable for investigating the genomewide evolutionary pattern of gene expression. To this end, phylogenetic expression analysis is highly desirable. On the basis of the Brownian process, we developed a statistical framework (called the E0 model), assuming the independent expression of evolution between lineages. Several evolutionary mechanisms are integrated to characterize the pattern of expression diversity after gene duplications, including gradual drift and dramatic shift (punctuated equilibrium). When the phylogeny of a gene family is given, we show that the likelihood function follows a multivariate normal distribution; the variance-covariance matrix is determined by the phylogenetic topology and evolutionary parameters. Maximum-likelihood methods for multiple microarray experiments are developed, and likelihood-ratio tests are designed for testing the evolutionary pattern of gene expression. To reconstruct the evolutionary trace of expression diversity after gene (or genome) duplications, we developed a Bayesian-based method and use the posterior mean as predictors. Potential applications in evolutionary genomics are discussed.

Publisher

Oxford University Press (OUP)

Subject

Genetics

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