dmGWAS: Dense module searching for genome-wide association studies in protein-protein interaction networks

Peilin Jia, Siyuan Zheng, Jirong Long, Wei Zheng, Zhongming Zhao

Research output: Contribution to journalArticlepeer-review

188 Scopus citations

Abstract

Motivation: An important question that has emerged from the recent success of genome-wide association studies (GWAS) is how to detect genetic signals beyond single markers/genes in order to explore their combined effects on mediating complex diseases and traits. Integrative testing of GWAS association data with that from prior-knowledge databases and proteome studies has recently gained attention. These methodologies may hold promise for comprehensively examining the interactions between genes underlying the pathogenesis of complex diseases. Methods: Here, we present a dense module searching (DMS) method to identify candidate subnetworks or genes for complex diseases by integrating the association signal from GWAS datasets into the human protein-protein interaction (PPI) network. The DMS method extensively searches for subnetworks enriched with low P-value genes in GWAS datasets. Compared with pathway-based approaches, this method introduces flexibility in defining a gene set and can effectively utilize local PPI information. Results: We implemented the DMS method in an R package, which can also evaluate and graphically represent the results. We demonstrated DMS in two GWAS datasets for complex diseases, i.e. breast cancer and pancreatic cancer. For each disease, the DMS method successfully identified a set of significant modules and candidate genes, including some well-studied genes not detected in the single-marker analysis of GWA studies. Functional enrichment analysis and comparison with previously published methods showed that the genes we identified by DMS have higher association signal.

Original languageEnglish (US)
Article numberbtq615
Pages (from-to)95-102
Number of pages8
JournalBioinformatics
Volume27
Issue number1
DOIs
StatePublished - Jan 2011

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'dmGWAS: Dense module searching for genome-wide association studies in protein-protein interaction networks'. Together they form a unique fingerprint.

Cite this