Document Detail

Time squared: repeated measures on phylogenies.
MedLine Citation:
PMID:  17079699     Owner:  NLM     Status:  MEDLINE    
Studies of gene expression profiles in response to external perturbation generate repeated measures data that generally follow nonlinear curves. To explore the evolution of such profiles across a gene family, we introduce phylogenetic repeated measures (PR) models. These models draw strength from 2 forms of correlation in the data. Through gene duplication, the family's evolutionary relatedness induces the first form. The second is the correlation across time points within taxonic units, individual genes in this example. We borrow a Brownian diffusion process along a given phylogenetic tree to account for the relatedness and co-opt a repeated measures framework to model the latter. Through simulation studies, we demonstrate that repeated measures models outperform the previously available approaches that consider the longitudinal observations or their differences as independent and identically distributed by using deviance information criteria as Bayesian model selection tools; PR models that borrow phylogenetic information also perform better than nonphylogenetic repeated measures models when appropriate. We then analyze the evolution of gene expression in the yeast kinase family using splines to estimate nonlinear behavior across 3 perturbation experiments. Again, the PR models outperform previous approaches and afford the prediction of ancestral expression profiles. To demonstrate PR model applicability more generally, we conclude with a short examination of variation in brain development across 4 primate species.
Hua Guo; Robert E Weiss; Xun Gu; Marc A Suchard
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Publication Detail:
Type:  Journal Article     Date:  2006-11-01
Journal Detail:
Title:  Molecular biology and evolution     Volume:  24     ISSN:  0737-4038     ISO Abbreviation:  Mol. Biol. Evol.     Publication Date:  2007 Feb 
Date Detail:
Created Date:  2007-01-31     Completed Date:  2007-05-16     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8501455     Medline TA:  Mol Biol Evol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  352-62     Citation Subset:  IM    
Department of Biostatistics, School of Public Health, University of California, Los Angeles, USA.
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MeSH Terms
Bayes Theorem
Brain / growth & development
Computer Simulation
Evolution, Molecular
Gene Expression Profiling
Models, Biological*
Models, Statistical*
Oligonucleotide Array Sequence Analysis
Phosphotransferases / genetics
Yeasts / enzymology,  genetics
Reg. No./Substance:
EC 2.7.-/Phosphotransferases

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