How to Cluster Gene Expression Dynamics in Response to Environmental Signals

Overview

Journal Brief Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2011 Jul 13

PMID 21746694

Citations 28

Authors

Yaqun Wang

Meng Xu

Zhong Wang

Ming Tao

Junjia Zhu

Li Wang

Runze Li

Scott A Berceli

Rongling Wu

Affiliations

Soon will be listed here.

Abstract

Organisms usually cope with change in the environment by altering the dynamic trajectory of gene expression to adjust the complement of active proteins. The identification of particular sets of genes whose expression is adaptive in response to environmental changes helps to understand the mechanistic base of gene-environment interactions essential for organismic development. We describe a computational framework for clustering the dynamics of gene expression in distinct environments through Gaussian mixture fitting to the expression data measured at a set of discrete time points. We outline a number of quantitative testable hypotheses about the patterns of dynamic gene expression in changing environments and gene-environment interactions causing developmental differentiation. The future directions of gene clustering in terms of incorporations of the latest biological discoveries and statistical innovations are discussed. We provide a set of computational tools that are applicable to modeling and analysis of dynamic gene expression data measured in multiple environments.

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