A sparse conditional Gaussian graphical model for analysis of genetical genomics data
From MaRDI portal
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.
Recommendations
- Sparse estimation of conditional graphical models with application to gene networks
- Sparse graphical models for exploring gene expression data
- Probabilistic graphical models for genetics, genomics and postgenomics
- A Bayesian graphical model for genome-wide association studies (GWAS)
- Graphical models for genetic analyses
- Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
- Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors
- Joint estimation of multiple dependent Gaussian graphical models with applications to mouse genomics
- On principal graphical models with application to gene network
- Information‐incorporated Gaussian graphical model for gene expression data
Cites work
- A sparse conditional Gaussian graphical model for analysis of genetical genomics data
- An Efficient Method of Estimating Seemingly Unrelated Regressions and Tests for Aggregation Bias
- Causal graphical models in systems genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes
- Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
- High-dimensional graphs and variable selection with the Lasso
- scientific article; zbMATH DE number 845714 (Why is no real title available?)
- Large-sample learning of Bayesian networks is NP-hard
- Model selection through sparse maximum likelihood estimation for multivariate Gaussian or binary data
- Network exploration via the adaptive LASSO and SCAD penalties
- Partial correlation estimation by joint sparse regression models
- Sparse inverse covariance estimation with the graphical lasso
- Sparsistency and rates of convergence in large covariance matrix estimation
- Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping
- The Adaptive Lasso and Its Oracle Properties
- Tuning parameter selectors for the smoothly clipped absolute deviation method
Cited in
(75)- Structural learning and estimation of joint causal effects among network-dependent variables
- cglasso
- A Penalized Likelihood Method for Classification With Matrix-Valued Predictors
- Generalized network psychometrics: combining network and latent variable models
- Variable selection and joint estimation of mean and covariance models with an application to eQTL data
- Modeling correlated marker effects in genome-wide prediction via Gaussian concentration graph models
- Sparse graphical models for exploring gene expression data
- Joint mean-covariance estimation via the horseshoe
- Multivariate sparse Laplacian shrinkage for joint estimation of two graphical structures
- On skewed Gaussian graphical models
- Estimation of conditional mean operator under the bandable covariance structure
- Meta-analytic Gaussian network aggregation
- Bayesian graphical models for modern biological applications
- Extending graphical models for applications: on covariates, missingness and normality
- A global-local approach for detecting hotspots in multiple-response regression
- Sparse directed acyclic graphs incorporating the covariates
- The conditional censored graphical Lasso estimator
- Capturing between-tasks covariance and similarities using multivariate linear mixed models
- Large-scale multiple inference of collective dependence with applications to protein function
- A covariance-enhanced approach to multitissue joint eQTL mapping with application to transcriptome-wide association studies
- A two-stage sequential conditional selection approach to sparse high-dimensional multivariate regression models
- Structured regularization for conditional Gaussian graphical models
- Node-structured integrative Gaussian graphical model guided by pathway information
- A penalized regression model for the joint estimation of eQTL associations and gene network structure
- Sparse conditional copula models for structured output regression
- An integrated precision matrix estimation for multivariate regression problems
- Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis
- A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis
- An Expectation Conditional Maximization Approach for Gaussian Graphical Models
- Simultaneous Variable and Covariance Selection With the Multivariate Spike-and-Slab LASSO
- Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
- 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
- A sparse Ising model with covariates
- Adjusting for high-dimensional covariates in sparse precision matrix estimation by _1-penalization
- Block-Diagonal Covariance Selection for High-Dimensional Gaussian Graphical Models
- Sparse estimation of conditional graphical models with application to gene networks
- scientific article; zbMATH DE number 7255095 (Why is no real title available?)
- High-dimensional Gaussian graphical models on network-linked data
- Bayesian Structure Learning in Multilayered Genomic Networks
- A partial graphical model with a structural prior on the direct links between predictors and responses
- Bayesian Estimation of Gaussian Conditional Random Fields
- An Explicit Mean-Covariance Parameterization for Multivariate Response Linear Regression
- Covariate-adjusted Gaussian graphical model estimation with false discovery rate control
- Graphical model selection for Gaussian conditional random fields in the presence of latent variables
- Joint estimation of multiple dependent Gaussian graphical models with applications to mouse genomics
- Low-Order Conditional Independence Graphs for Inferring Genetic Networks
- Variable screening in multivariate linear regression with high-dimensional covariates
- Assessment of Covariance Selection Methods in High-Dimensional Gaussian Graphical Models
- High-Dimensional Gaussian Graphical Regression Models with Covariates
- Information‐incorporated Gaussian graphical model for gene expression data
- A new covariate selection strategy for high dimensional data in causal effect estimation with multivariate treatments
- Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data
- Robust Multivariate Lasso Regression with Covariance Estimation
- Estimation and inference in sparse multivariate regression and conditional Gaussian graphical models under an unbalanced distributed setting
- Bayesian feature selection in high-dimensional regression in presence of correlated noise
- Semiparametric Bayes conditional graphical models for imaging genetics applications
- Response variable selection in multivariate linear regression
- Conditional Gaussian graphical model for estimating personalized disease symptom networks
- Integrating approximate single factor graphical models
- Covariate-Assisted Bayesian Graph Learning for Heterogeneous Data
- Bayesian robust learning in chain graph models for integrative pharmacogenomics
- Regulation-incorporated gene expression network-based heterogeneity analysis
- Density and graph estimation with smoothing splines and conditional Gaussian graphical models
- Conditional graphical models with a hierarchical sparse estimation
- Estimation of the error structure in multivariate response linear regression models
- Generalized score matching
- High-dimensional graphical inference via partially penalised regression
- Sparse inference of the human haematopoietic system from heterogeneous and partially observed genomic data
- Fast autoregressive model for multivariate dependent outcomes with application to lipidomics analysis for Alzheimer's disease and APOE- 4
- A sparse conditional Gaussian graphical model for analysis of genetical genomics data
- Ensemble sparse estimation of covariance structure for exploring genetic disease data
- Causal graphical models in systems genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes
- Of mice and men: sparse statistical modeling in cardiovascular genomics
This page was built for publication: A sparse conditional Gaussian graphical model for analysis of genetical genomics data
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q80801)
