More power via graph-structured tests for differential expression of gene networks

DOI10.1214/11-AOAS528zbMATH Open1243.62080arXiv1206.6980MaRDI QIDQ439146FDOQ439146

Authors: Laurent Jacob, Pierre Neuvial, Sandrine Dudoit 

Publication date: 1 August 2012

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

Abstract: We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially expressed genes between two patient populations, as shifts in expression levels are expected to be coherent with the structure of graphs reflecting gene properties such as biological process, molecular function, regulation or metabolism. For a fixed graph of interest, we demonstrate that accounting for graph structure can yield more powerful tests under the assumption of smooth distribution shift on the graph. We also investigate the identification of nonhomogeneous subgraphs of a given large graph, which poses both computational and multiple hypothesis testing problems. The relevance and benefits of the proposed approach are illustrated on synthetic data and on breast and bladder cancer gene expression data analyzed in the context of KEGG and NCI pathways.

Full work available at URL: https://arxiv.org/abs/1206.6980

Recommendations

• Combined hypothesis testing on graphs with applications to gene set enrichment analysis
• Network differential connectivity analysis
• A test for partial differential expression
• A multiple testing method for hypotheses structured in a directed acyclic graph
• Testing differential networks with applications to the detection of gene-gene interactions

zbMATH Keywords

spectral graph theorydimensionality reductiontwo-sample testbiological networksgraph Laplacianenrichment analysisHotelling T2pathways

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of graph theory (05C90) Hypothesis testing in multivariate analysis (62H15) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Cites Work

• Title not available (Why is that?)
• Wavelets on graphs via spectral graph theory
• Title not available (Why is that?)
• Test of Significance When Data Are Curves
• A two-sample test for high-dimensional data with applications to gene-set testing
• Multiple testing procedures with applications to genomics.
• An Automatic Method of Solving Discrete Programming Problems
• Title not available (Why is that?)
• A test for the mean vector with fewer observations than the dimension under non-normality
• A test for the mean vector with fewer observations than the dimension
• Title not available (Why is that?)
• Structured variable selection with sparsity-inducing norms
• Power of the Noncentral F-Test: Effect of Additional Variates on Hotelling's T 2 -Test
• Stable feature selection for biomarker discovery
• Title not available (Why is that?)
• More power via graph-structured tests for differential expression of gene networks
• Some new bounds on perturbation of subspaces
• On Gene Ranking Using Replicated Microarray Time Course Data

Cited In (9)

• A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
• More power via graph-structured tests for differential expression of gene networks
• Tests for differential Gaussian Bayesian networks based on quadratic inference functions
• A high-dimensional two-sample test for the mean using random subspaces
• Covariate-adjusted inference for differential analysis of high-dimensional networks
• Combined hypothesis testing on graphs with applications to gene set enrichment analysis
• Gaussian Bayesian network comparisons with graph ordering unknown
• Comparing dependent undirected Gaussian networks
• A review of 20 years of naive tests of significance for high-dimensional mean vectors and covariance matrices

Uses Software

• NCIgraph
• GOstat
• KEGG
• HotNet

This page was built for publication: More power via graph-structured tests for differential expression of gene networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q439146)