Sparse factor model for co-expression networks with an application using prior biological knowledge

DOI10.1515/SAGMB-2015-0002MaRDI QIDQ306641zbMATH OpenOpenAlexWikidataFDO

Authors Yuna Blum, Magalie Houée-Bigot, David Causeur

Publication date 1 September 2016

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1515/sagmb-2015-0002

zbMATH Keywords

factor modelsparsityregularized estimationhigh dimensiongene ontologyrelevance network

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15) Genetics and epigenetics (92D10) Systems biology, networks (92C42) Software, source code, etc. for problems pertaining to information and communication theory (94-04)

Recommendations

• High-dimensional sparse factor modeling: applications in gene expression genomics
• Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
• Sparse graphical models for exploring gene expression data
• Sparse regulatory networks
• Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks

Cites work

• scientific article; zbMATH DE number 3567782 (Why is no real title available?)
• A General Framework for Weighted Gene Co-Expression Network Analysis
• A factor model approach to multiple testing under dependence
• A general framework for multiple testing dependence
• A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
• A survey of statistical network models
• Coordinate descent algorithms for lasso penalized regression
• EM algorithms for ML factor analysis
• (SOFTWARE) FAMT
• High-dimensional sparse factor modeling: applications in gene expression genomics
• Model selection through sparse maximum likelihood estimation for multivariate Gaussian or binary data
• Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data
• Note on “Comparison of Model Selection for Regression” by Vladimir Cherkassky and Yunqian Ma
• Sparse inverse covariance estimation with the graphical lasso

Cited in

(4)

• High-dimensional sparse factor modeling: applications in gene expression genomics
• Sparse regulatory networks
• A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate
• Inferring gene-gene interactions and functional modules using sparse canonical correlation analysis

Describes a project that uses

Uses Software

• PMA
• leapp
• FAMT
• dynamicTreeCut
• glmnet
• glasso
• WGCNA

This page was built for publication: Sparse factor model for co-expression networks with an application using prior biological knowledge

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q306641)