Journal
BRIEFINGS IN BIOINFORMATICS
Volume 13, Issue 2, Pages 162-174Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbr032
Keywords
dynamic gene expression; functional clustering; gene-environment interaction; mixture model
Funding
- NIH/NHLBI [R01 HL095508]
- NIDA/NIH [R21-DA024260, P50-DA10075]
- National Natural Science Foundation of China [11028103]
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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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