Link to the University of Pittsburgh Homepage
Link to the University Library System Homepage Link to the Contact Us Form

Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies

Wang, Q and Jia, P and Cuenco, KT and Zeng, Z and Feingold, E and Marazita, ML and Wang, L and Zhao, Z (2013) Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies. PLoS ONE, 8 (8).

[img]
Preview
PDF
Published Version
Available under License : See the attached license file.

Download (186kB) | Preview
[img] Plain Text (licence)
Available under License : See the attached license file.

Download (1kB)

Abstract

Gene set-based analysis of genome-wide association study (GWAS) data has recently emerged as a useful approach to examine the joint effects of multiple risk loci in complex human diseases or phenotypes. Dental caries is a common, chronic, and complex disease leading to a decrease in quality of life worldwide. In this study, we applied the approaches of gene set enrichment analysis to a major dental caries GWAS dataset, which consists of 537 cases and 605 controls. Using four complementary gene set analysis methods, we analyzed 1331 Gene Ontology (GO) terms collected from the Molecular Signatures Database (MSigDB). Setting false discovery rate (FDR) threshold as 0.05, we identified 13 significantly associated GO terms. Additionally, 17 terms were further included as marginally associated because they were top ranked by each method, although their FDR is higher than 0.05. In total, we identified 30 promising GO terms, including 'Sphingoid metabolic process,' 'Ubiquitin protein ligase activity,' 'Regulation of cytokine secretion,' and 'Ceramide metabolic process.' These GO terms encompass broad functions that potentially interact and contribute to the oral immune response related to caries development, which have not been reported in the standard single marker based analysis. Collectively, our gene set enrichment analysis provided complementary insights into the molecular mechanisms and polygenic interactions in dental caries, revealing promising association signals that could not be detected through single marker analysis of GWAS data. © 2013 Wang et al.


Share

Citation/Export:
Social Networking:
Share |

Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Wang, Q
Jia, P
Cuenco, KTktc14@pitt.eduKTC14
Zeng, Zzhz43@pitt.eduZHZ43
Feingold, Efeingold@pitt.eduFEINGOLD
Marazita, MLmarazita@pitt.eduMARAZITA
Wang, L
Zhao, Z
Date: 14 August 2013
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 8
Number: 8
DOI or Unique Handle: 10.1371/journal.pone.0072653
Schools and Programs: Graduate School of Public Health > Human Genetics
Refereed: Yes
Date Deposited: 23 Sep 2013 17:17
Last Modified: 04 Feb 2019 15:56
URI: http://d-scholarship.pitt.edu/id/eprint/19770

Metrics

Monthly Views for the past 3 years

Plum Analytics

Altmetric.com


Actions (login required)

View Item View Item