Inferring gene-gene interactions and functional modules using sparse canonical correlation analysis
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Publication:2349574
DOI10.1214/14-AOAS792zbMATH Open1454.62416arXiv1401.6504OpenAlexW2053404654MaRDI QIDQ2349574FDOQ2349574
Publication date: 17 June 2015
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Networks pervade many disciplines of science for analyzing complex systems with interacting components. In particular, this concept is commonly used to model interactions between genes and identify closely associated genes forming functional modules. In this paper, we focus on gene group interactions and infer these interactions using appropriate partial correlations between genes, that is, the conditional dependencies between genes after removing the influences of a set of other functionally related genes. We introduce a new method for estimating group interactions using sparse canonical correlation analysis (SCCA) coupled with repeated random partition and subsampling of the gene expression data set. By considering different subsets of genes and ways of grouping them, our interaction measure can be viewed as an aggregated estimate of partial correlations of different orders. Our approach is unique in evaluating conditional dependencies when the correct dependent sets are unknown or only partially known. As a result, a gene network can be constructed using the interaction measures as edge weights and gene functional groups can be inferred as tightly connected communities from the network. Comparisons with several popular approaches using simulated and real data show our procedure improves both the statistical significance and biological interpretability of the results. In addition to achieving considerably lower false positive rates, our procedure shows better performance in detecting important biological pathways.
Full work available at URL: https://arxiv.org/abs/1401.6504
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partial correlationcommunity structuregene association networkssparse canonical correlation analysis (SCCA)
Applications of statistics to biology and medical sciences; meta analysis (62P10) Measures of association (correlation, canonical correlation, etc.) (62H20) Genetics and epigenetics (92D10)
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Cited In (9)
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- Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information
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