ArticleBMC genomics2011
Expression divergence measured by transcriptome sequencing of four yeast species.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Transcriptomic Analysis Reveals HowLife (Basel, Switzerland) · 2026Article
- PAGE: an R package for network detection of multivariate error-prone gene expression data with the availability of auxiliary information.BMC bioinformatics · 2026Article
- Revisiting the use of structural similarity index in Hi-C.Nature genetics · 2023Article
- MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.Nature communications · 2021Article
- Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes.BMC plant biology · 2020Article
- A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.Genome biology and evolution · 2016Article
- Gene Regulatory Evolution During Speciation in a Songbird.G3 (Bethesda, Md.) · 2016Article
- Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing.FEBS open bio · 2016Article
- Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.BMC genomics · 2015Article
- Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.Molecular biology and evolution · 2015Article
- Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.BMC genomics · 2014Article
- Independent stratum formation on the avian sex chromosomes reveals inter-chromosomal gene conversion and predominance of purifying selection on the W chromosome.Evolution; international journal of organic evolution · 2014Article
- Evolution of splicing regulatory networks in Drosophila.Genome research · 2014Article
- Tempo and mode of regulatory evolution in Drosophila.Genome research · 2014Article
- Article
- Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula.PLoS neglected tropical diseases · 2013Article
- Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.PLoS computational biology · 2013Article
- Inferring evolutionary histories of pathway regulation from transcriptional profiling data.PLoS computational biology · 2013Article
- Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome.Genetics · 2012Article
- Candida albicans: A Model Organism for Studying Fungal Pathogens.ISRN microbiology · 2012Article
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9 authors.
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Abstract
backgroundThe evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.
resultsWe quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of Saccharomyces species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R² = 0.90).
conclusionWe provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.GEO Accession Number: GSE32679.
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