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13:17
Microarray Analysis for Saccharomyces cerevisiae
Published on: April 7, 2011
Comparative gene expression between two yeast species.
Yuanfang Guan1, Maitreya J Dunham, Olga G Troyanskaya
1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
BMC Genomics
|January 18, 2013
Summary
Comparative genomics reveals gene expression patterns between Saccharomyces species. While sequence and expression are globally conserved, gene expression neighborhoods and co-expression partners show divergence, offering insights into genomic regulation.
Area of Science:
- Comparative genomics
- Systems biology
- Evolutionary biology
Background:
- Limited understanding of gene function and regulation across species hinders comparative genomics.
- Biased sampling of expression conditions affects the reliability of cross-species comparisons.
- Systematic generation of expression profiles in Saccharomyces bayanus aimed to improve functional coverage.
Purpose of the Study:
- To compare ortholog expression patterns between Saccharomyces cerevisiae and Saccharomyces bayanus across diverse conditions.
- To develop a scalable metric for quantifying expression divergence.
- To investigate the conservation of gene expression neighborhoods and co-expression partners.
Main Methods:
- Utilized existing Saccharomyces cerevisiae and newly generated Saccharomyces bayanus expression data repositories.
- Developed and applied a scalable metric for expression divergence analysis.
- Compared between-species and within-species gene expression patterns under various environmental perturbations.
Main Results:
- Detected a significant global correlation between sequence and expression conservation.
- Observed less conserved gene expression neighborhoods between species compared to within species.
- Identified approximately 4% of orthologs with altered co-expression partners and a quarter with condition-specific expression differences.
Conclusions:
- Provided a global perspective on inter-species gene expression patterns, including timing and co-expression.
- Generated testable hypotheses for future research into the genomic basis of expression changes.
- Highlighted the dynamic nature of gene regulation and co-expression across related species.
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