A sparse conditional Gaussian graphical model for analysis of genetical genomics data

DOI10.1214/11-AOAS494zbMATH Open1234.62151arXiv1202.6515OpenAlexW2018747370WikidataQ34384169 ScholiaQ34384169MaRDI QIDQ80801FDOQ80801

Hongzhe Li, Jianxing Yin, Jianxin Yin, Hongzhe Li

Publication date: 1 December 2011

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Genetical genomics experiments have now been routinely conducted to measure both the genetic markers and gene expression data on the same subjects. The gene expression levels are often treated as quantitative traits and are subject to standard genetic analysis in order to identify the gene expression quantitative loci (eQTL). However, the genetic architecture for many gene expressions may be complex, and poorly estimated genetic architecture may compromise the inferences of the dependency structures of the genes at the transcriptional level. In this paper we introduce a sparse conditional Gaussian graphical model for studying the conditional independent relationships among a set of gene expressions adjusting for possible genetic effects where the gene expressions are modeled with seemingly unrelated regressions. We present an efficient coordinate descent algorithm to obtain the penalized estimation of both the regression coefficients and the sparse concentration matrix. The corresponding graph can be used to determine the conditional independence among a group of genes while adjusting for shared genetic effects. Simulation experiments and asymptotic convergence rates and sparsistency are used to justify our proposed methods. By sparsistency, we mean the property that all parameters that are zero are actually estimated as zero with probability tending to one. We apply our methods to the analysis of a yeast eQTL data set and demonstrate that the conditional Gaussian graphical model leads to a more interpretable gene network than a standard Gaussian graphical model based on gene expression data alone.

Full work available at URL: https://arxiv.org/abs/1202.6515

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zbMATH Keywords

regularizationeQTLgenetic networksseemingly unrelated regression

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Applications of graph theory (05C90) Estimation in multivariate analysis (62H12) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

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Cited In (60)

• Adjusting for high-dimensional covariates in sparse precision matrix estimation by \(\ell_1\)-penalization
• Capturing between-tasks covariance and similarities using multivariate linear mixed models
• Bayesian Structure Learning in Multilayered Genomic Networks
• Structured regularization for conditional Gaussian graphical models
• Joint mean-covariance estimation via the horseshoe
• Multivariate sparse Laplacian shrinkage for joint estimation of two graphical structures
• Title not available (Why is that?)
• Ensemble sparse estimation of covariance structure for exploring genetic disease data
• Node-structured integrative Gaussian graphical model guided by pathway information
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• Generalized network psychometrics: combining network and latent variable models
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• Meta-analytic Gaussian network aggregation
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• An Expectation Conditional Maximization Approach for Gaussian Graphical Models
• Simultaneous Variable and Covariance Selection With the Multivariate Spike-and-Slab LASSO
• Multivariate sparse group lasso for the multivariate multiple linear regression with an arbitrary group structure
• Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies
• Sparse canonical correlation analysis from a predictive point of view
• Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis
• A sparse conditional Gaussian graphical model for analysis of genetical genomics data
• A new covariate selection strategy for high dimensional data in causal effect estimation with multivariate treatments
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• Structural learning and estimation of joint causal effects among network-dependent variables
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Uses Software

• glasso
• KEGG

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