Module-based association analysis for omics data with network structure.

Published online

Journal Article

Module-based analysis (MBA) aims to evaluate the effect of a group of biological elements sharing common features, such as SNPs in the same gene or metabolites in the same pathways, and has become an attractive alternative to traditional single bio-element approaches. Because bio-elements regulate and interact with each other as part of network, incorporating network structure information can more precisely model the biological effects, enhance the ability to detect true associations, and facilitate our understanding of the underlying biological mechanisms. However, most MBA methods ignore the network structure information, which depicts the interaction and regulation relationship among basic functional units in biology system. We construct the connectivity kernel and the topology kernel to capture the relationship among bio-elements in a module, and use a kernel machine framework to evaluate the joint effect of bio-elements. Our proposed kernel machine approach directly incorporates network structure so to enhance the study efficiency; it can assess interactions among modules, account covariates, and is computational efficient. Through simulation studies and real data application, we demonstrate that the proposed network-based methods can have markedly better power than the approaches ignoring network information under a range of scenarios.

Full Text

Duke Authors

Cited Authors

  • Wang, Z; Maity, A; Hsiao, CK; Voora, D; Kaddurah-Daouk, R; Tzeng, J-Y

Published Date

  • 2015

Published In

Volume / Issue

  • 10 / 3

Start / End Page

  • e0122309 -

PubMed ID

  • 25822417

Pubmed Central ID

  • 25822417

Electronic International Standard Serial Number (EISSN)

  • 1932-6203

Digital Object Identifier (DOI)

  • 10.1371/journal.pone.0122309

Language

  • eng

Conference Location

  • United States