ArticleTheoretical population biology2010
Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions.
Article in Theoretical population biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Genome-scale metabolic modelling identifies reactions mediated by SNP-SNP interactions associated with yeast sporulation.NPJ systems biology and applications · 2025Article
- Article
- A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models.Bioinformatics (Oxford, England) · 2020Article
- Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation.PloS one · 2019Article
- Modeling of a negative feedback mechanism explains antagonistic pleiotropy in reproduction in domesticated Caenorhabditis elegans strains.PLoS genetics · 2017Article
- Predicting quantitative traits from genome and phenome with near perfect accuracy.Nature communications · 2016Article
- A survey about methods dedicated to epistasis detection.Frontiers in genetics · 2015Review
- Cis-regulatory elements and human evolution.Current opinion in genetics & development · 2014Review
- Dominant PRPF31 mutations are hypostatic to a recessive CNOT3 polymorphism in retinitis pigmentosa: a novel phenomenon of "linked trans-acting epistasis".Annals of human genetics · 2014Article
- Bridging the genotype-phenotype gap: what does it take?The Journal of physiology · 2013Review
- Effect of regulatory architecture on broad versus narrow sense heritability.PLoS computational biology · 2013Article
- Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration.PLoS genetics · 2012Article
- Use of a predictive model derived from in vivo endophenotype measurements to demonstrate associations with a complex locus, CYP2A6.Human molecular genetics · 2012Article
- Comparative studies of gene expression and the evolution of gene regulation.Nature reviews. Genetics · 2012Review
- Parameters in dynamic models of complex traits are containers of missing heritability.PLoS computational biology · 2012Article
- Thermodynamic state ensemble models of cis-regulation.PLoS computational biology · 2012Article
- Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast.Comparative and functional genomics · 2012Article
- Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi.BMC bioinformatics · 2011Article
- Gene-environment interactions at nucleotide resolution.PLoS genetics · 2010Article
- Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies.Wiley interdisciplinary reviews. Systems biology and medicineReview
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3 authors.
Funding
Abstract
With technological advances in genetic mapping studies more of the genes and polymorphisms that underlie Quantitative Trait Loci (QTL) are now being identified. As the identities of these genes become known there is a growing need for an analysis framework that incorporates the molecular interactions affected by natural polymorphisms. As a step towards such a framework we present a molecular model of genetic variation in sporulation efficiency between natural isolates of the yeast, Saccharomyces cerevisiae. The model is based on the structure of the regulatory pathway that controls sporulation. The model captures the phenotypic variation between strains carrying different combinations of alleles at known QTL. Compared to a standard linear model the molecular model requires fewer free parameters, and has the advantage of generating quantitative hypotheses about the affinity of specific molecular interactions in different genetic backgrounds. Our analyses provide a concrete example of how the thermodynamic properties of protein-protein and protein-DNA interactions naturally give rise to epistasis, the non-linear relationship between genotype and phenotype. As more causative genes and polymorphisms underlying QTL are identified, thermodynamic analyses of quantitative traits may provide a useful framework for unraveling the complex relationship between genotype and phenotype.
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