scholarly journals Comparative Methods for the Analysis of Gene-Expression Evolution: An Example Using Yeast Functional Genomic Data

2004 ◽  
Vol 22 (1) ◽  
pp. 40-50 ◽  
Author(s):  
Todd H. Oakley ◽  
Zhenglong Gu ◽  
Ehab Abouheif ◽  
Nipam H. Patel ◽  
Wen-Hsiung Li
Keyword(s):  
Gene Expression ◽  
Genomic Data ◽  
Comparative Methods ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Expression Evolution ◽  
Gene Expression Evolution

scholarly journals Pairwise comparisons across species are problematic when analyzing functional genomic data

2017 ◽  
Author(s):  
Casey W. Dunn ◽  
Felipe Zapata ◽  
Catriona Munro ◽  
Stefan Siebert ◽  
Andreas Hejnol
Keyword(s):  
Gene Expression ◽  
Evolutionary Process ◽  
Opportunity To Learn ◽  
Genomic Data ◽  
The Other ◽  
Evolutionary Relationships ◽  
Pairwise Comparisons ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Comparative Functional Genomics

AbstractThere is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions, and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to be more similar than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead we find they reflect species relationships. These reanalyses concretely demonstrate the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.SignificanceComparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here we demonstrate that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We re-examined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study had found support for the ortholog conjecture and the other had concluded that the evolution of gene expression was different between animal phyla than within them. Our results demonstrate that to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.

scholarly journals Pairwise comparisons across species are problematic when analyzing functional genomic data

2018 ◽  
Vol 115 (3) ◽  
pp. E409-E417 ◽  
Author(s):  
Casey W. Dunn ◽  
Felipe Zapata ◽  
Catriona Munro ◽  
Stefan Siebert ◽  
Andreas Hejnol
Keyword(s):  
Gene Expression ◽  
Evolutionary Process ◽  
Opportunity To Learn ◽  
Genomic Data ◽  
Pairwise Comparisons ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Genomic Studies ◽  
Compare Gene Expression ◽  
Missed Opportunity

There is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here, we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to have more similar attributes (expression in this case) than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead, we find that they reflect species relationships. These reanalyses concretely show the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.

scholarly journals Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

2008 ◽  
Vol 40 (7) ◽  
pp. 854-861 ◽  
Author(s):  
Jun Zhu ◽  
Bin Zhang ◽  
Erin N Smith ◽  
Becky Drees ◽  
Rachel B Brem ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

scholarly journals Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

2011 ◽  
Vol 7 (6) ◽  
pp. e1002073 ◽  
Author(s):  
Nathan L. Nehrt ◽  
Wyatt T. Clark ◽  
Predrag Radivojac ◽  
Matthew W. Hahn
Keyword(s):  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

scholarly journals Relating gene expression evolution with CpG content changes

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 693 ◽  
Author(s):  
Huan Yang ◽  
Dawei Li ◽  
Chao Cheng
Keyword(s):  
Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

scholarly journals Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

2014 ◽  
Vol 24 (7) ◽  
pp. 1115-1124 ◽  
Author(s):  
R. K. Arthur ◽  
L. Ma ◽  
M. Slattery ◽  
R. F. Spokony ◽  
A. Ostapenko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Expression Evolution ◽  
Gene Expression Evolution
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