ArticleGenome biology and evolution2010
Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 34 citations in OpenAlex.
- Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.Nature communications · 2020Article
- Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.Nucleic acids research · 2020Article
- Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.PloS one · 2018Article
- Cis-regulatory evolution in a wild primate: Infection-associated genetic variation drives differential expression of MHC-DQA1 in vitro.Molecular ecology · 2017Article
- Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.BMC genomics · 2017Article
- Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species.Genome biology and evolution · 2017Article
- Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.Genome biology and evolution · 2015Article
- Biophysical fitness landscapes for transcription factor binding sites.PLoS computational biology · 2014Article
- Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells.BioData mining · 2014Article
- The molecular basis of phenotypic variation in yeast.Current opinion in genetics & development · 2013Review
- Mapping yeast transcriptional networks.Genetics · 2013Review
- Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains.Molecular biology and evolution · 2013Article
- Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus).Ecology and evolution · 2013Article
- SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.Nucleic acids research · 2013Article
- Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.PLoS computational biology · 2013Article
- Local ancestry corrects for population structure in Saccharomyces cerevisiae genome-wide association studies.Genetics · 2012Article
- Analysis of variation at transcription factor binding sites in Drosophila and humans.Genome biology · 2012Article
- SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig.BMC genetics · 2012Article
- Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.PloS one · 2012Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 4 countries.
Funding
Abstract
Identifying the nucleotides that cause gene expression variation is a critical step in dissecting the genetic basis of complex traits. Here, we focus on polymorphisms that are predicted to alter transcription factor binding sites (TFBSs) in the yeast, Saccharomyces cerevisiae. We assembled a confident set of transcription factor motifs using recent protein binding microarray and ChIP-chip data and used our collection of motifs to predict a comprehensive set of TFBSs across the S. cerevisiae genome. We used a population genomics analysis to show that our predictions are accurate and significantly improve on our previous annotation. Although predicting gene expression from sequence is thought to be difficult in general, we identified a subset of genes for which changes in predicted TFBSs correlate well with expression divergence between yeast strains. Our analysis thus demonstrates both the accuracy of our new TFBS predictions and the feasibility of using simple models of gene regulation to causally link differences in gene expression to variation at individual nucleotides.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.