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A comprehensive analysis of gene expression evolution between humans and mice.

Wang Y, Rekaya R - Evol. Bioinform. Online (2009)

Bottom Line: In this study, gene expression patterns were compared between human and mouse genomes using two published methods.The results showed that (1) the significant enrichment of biological processes in orthologs of expression conservation reveals functional significance of gene expression conservation.Our results suggest a neutral model with negative selection for gene expression evolution between humans and mice, and promoter evolution could have some effects on gene expression evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA.

ABSTRACT
Evolutionary changes in gene expression account for most phenotypic differences between species. Advances in microarray technology have made the systematic study of gene expression evolution possible. In this study, gene expression patterns were compared between human and mouse genomes using two published methods. Specifically, we studied how gene expression evolution was related to GO terms and tried to decode the relationship between promoter evolution and gene expression evolution. The results showed that (1) the significant enrichment of biological processes in orthologs of expression conservation reveals functional significance of gene expression conservation. The more conserved gene expression in some biological processes than is expected in a purely neutral model reveals negative selection on gene expression. However, fast evolving genes mainly support the neutrality of gene expression evolution, and (2) gene expression conservation is positively but only slightly correlated with promoter conservation based on a motif-count score of the promoter alignment. Our results suggest a neutral model with negative selection for gene expression evolution between humans and mice, and promoter evolution could have some effects on gene expression evolution.

No MeSH data available.


Distribution of Z-scores for GO terms.
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f1-ebo-2009-081: Distribution of Z-scores for GO terms.

Mentions: To further validate the evolutionary model of gene expression, we investigated how all available GO terms affected gene expression evolution. We took all the orthologous gene pairs as a population and grouped orthologous gene pairs by GO terms. We selected the GO terms with no less than three members and tested 320 terms in all. For each term, we got a Z-score for the mean correlation. Theoretically, these Z-scores should follow a standard normal distribution if no selection exists (note that we removed the GO terms with only one or two members because the means of small size samples may not form the normal distribution if the population does not agree with an exact normal distribution). We plotted the distribution of Z-scores of GO terms against a standard normal distribution (Fig. 1). Generally, the curves formed by procedure I and II fit the neutral model. The distribution of Z-scores for procedure I or II tends to have a heavier right tail (the part of the Z-score >1.96) compared to the control, suggesting that a small part of GO terms have negative selection on gene expression. However, a left heavier tail (the part of the Z-score <−1.96) is not observed, suggesting that generally GO terms do not have obvious positive selection on gene expression.


A comprehensive analysis of gene expression evolution between humans and mice.

Wang Y, Rekaya R - Evol. Bioinform. Online (2009)

Distribution of Z-scores for GO terms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2747126&req=5

f1-ebo-2009-081: Distribution of Z-scores for GO terms.
Mentions: To further validate the evolutionary model of gene expression, we investigated how all available GO terms affected gene expression evolution. We took all the orthologous gene pairs as a population and grouped orthologous gene pairs by GO terms. We selected the GO terms with no less than three members and tested 320 terms in all. For each term, we got a Z-score for the mean correlation. Theoretically, these Z-scores should follow a standard normal distribution if no selection exists (note that we removed the GO terms with only one or two members because the means of small size samples may not form the normal distribution if the population does not agree with an exact normal distribution). We plotted the distribution of Z-scores of GO terms against a standard normal distribution (Fig. 1). Generally, the curves formed by procedure I and II fit the neutral model. The distribution of Z-scores for procedure I or II tends to have a heavier right tail (the part of the Z-score >1.96) compared to the control, suggesting that a small part of GO terms have negative selection on gene expression. However, a left heavier tail (the part of the Z-score <−1.96) is not observed, suggesting that generally GO terms do not have obvious positive selection on gene expression.

Bottom Line: In this study, gene expression patterns were compared between human and mouse genomes using two published methods.The results showed that (1) the significant enrichment of biological processes in orthologs of expression conservation reveals functional significance of gene expression conservation.Our results suggest a neutral model with negative selection for gene expression evolution between humans and mice, and promoter evolution could have some effects on gene expression evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA.

ABSTRACT
Evolutionary changes in gene expression account for most phenotypic differences between species. Advances in microarray technology have made the systematic study of gene expression evolution possible. In this study, gene expression patterns were compared between human and mouse genomes using two published methods. Specifically, we studied how gene expression evolution was related to GO terms and tried to decode the relationship between promoter evolution and gene expression evolution. The results showed that (1) the significant enrichment of biological processes in orthologs of expression conservation reveals functional significance of gene expression conservation. The more conserved gene expression in some biological processes than is expected in a purely neutral model reveals negative selection on gene expression. However, fast evolving genes mainly support the neutrality of gene expression evolution, and (2) gene expression conservation is positively but only slightly correlated with promoter conservation based on a motif-count score of the promoter alignment. Our results suggest a neutral model with negative selection for gene expression evolution between humans and mice, and promoter evolution could have some effects on gene expression evolution.

No MeSH data available.