Inference and characterization of multi-attribute networks with application to computational biology

DOI10.1214/12-AOAS550zbMATH Open1254.92035arXiv1109.3160MaRDI QIDQ714366FDOQ714366

Eric D. Kolaczyk, Natallia Katenka

Publication date: 21 October 2012

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

Abstract: Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements, where a link between two different elements indicates a sufficient level of similarity between element attributes. While in reality relational ties between elements can be expected to be based on similarity across multiple attributes, the vast majority of work to date on association networks involves ties defined with respect to only a single attribute. We propose an approach for the inference of multi-attribute association networks from measurements on continuous attribute variables, using canonical correlation and a hypothesis-testing strategy. Within this context, we then study the impact of partial information on multi-attribute network inference and characterization, when only a subset of attributes is available. We consider in detail the case of two attributes, wherein we examine through a combination of analytical and numerical techniques the implications of the choice and number of node attributes on the ability to detect network links and, more generally, to estimate higher-level network summary statistics, such as node degree, clustering coefficients, and measures of centrality. Illustration and applications throughout the paper are developed using gene and protein expression measurements on human cancer cell lines from the NCI-60 database.

Full work available at URL: https://arxiv.org/abs/1109.3160

zbMATH Keywords

canonical correlationsgene/protein regulatory networksmulti-attribute association networks

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Measures of association (correlation, canonical correlation, etc.) (62H20) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Computational methods for problems pertaining to biology (92-08)

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Cited In (4)

• Scalable module detection for attributed networks with applications to breast cancer
• Bootstrap inference for network construction with an application to a breast cancer microarray study
• Estimation of graphical models: an overview of selected topics
• Molecular multiplex network inference using Gaussian mixture hidden Markov models

Uses Software

• KEGG

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