Module-based association analysis for omics data with network structure

Zhi Wang, Arnab Maity, Chuhsing Kate Hsiao, Deepak Voora, Rima Kaddurah-Daouk, Jung Ying Tzeng

研究成果: Article同行評審

7 引文 斯高帕斯(Scopus)

摘要

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. How-ever, 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 con-nectivity kernel and the topology kernel to capture the relationship among bio-elements in a mod-ule, 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 effi-ciency; it can assess interactions among modules, account covariates, and is computational effi-cient. 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.

原文English
文章編號e0122309
期刊PloS one
10
發行號3
DOIs
出版狀態Published - 2015 3月 30

All Science Journal Classification (ASJC) codes

  • 生物化學、遺傳與分子生物學 (全部)
  • 農業與生物科學 (全部)
  • 多學科

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