Tur Mongé, Imma, 1985-Roverato, AlbertoCastelo Valdueza, Robert2025-06-062025-06-062014Tur I, Roverato A, Castelo R. Mapping eQTL networks with mixed graphical Markov models. Genetics. 2014 Dec 1;198(4):1377-93. DOI: 10.1534/genetics.114.1695730016-6731http://hdl.handle.net/10230/70637Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by confounding factors and other sources of unwanted variation, indirect effects spread throughout genes as a result of genetic, molecular, and environmental perturbations. From a multivariate perspective one would like to adjust for the effect of all of these factors to end up with a network of direct associations connecting the path from genotype to phenotype. In this article we approach this challenge with mixed graphical Markov models, higher-order conditional independences, and q-order correlation graphs. These models show that additive genetic effects propagate through the network as function of gene–gene correlations. Our estimation of the eQTL network underlying a well-studied yeast data set leads to a sparse structure with more direct genetic and regulatory associations that enable a straightforward comparison of the genetic control of gene expression across chromosomes. Interestingly, it also reveals that eQTLs explain most of the expression variability of network hub genes.application/pdfeng© Oxford University Press. This is a pre-copyedited, author-produced version of an article accepted for publication in Genetics following peer review. The version of record Tur I, Roverato A, Castelo R. Mapping eQTL networks with mixed graphical Markov models. Genetics. 2014 Dec 1;198(4):1377-93. DOI: 10.1534/genetics.114.169573 is available online at: https://academic.oup.com/genetics/article/198/4/1377/5935964 and https://doi.org/10.1534/genetics.114.169573.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1534/genetics.114.169573eQTLGene networkExact-likelihood-ratio testConditional Gaussian distributionMixed graphical Markov modelinfo:eu-repo/semantics/openAccess