EINVis: A Visualization Tool for Analyzing and Exploring Genetic Interactions in Large-Scale Association Studies
Article first published online: 11 AUG 2013
© 2013 WILEY PERIODICALS, INC.
Volume 37, Issue 7, pages 675–685, November 2013
How to Cite
Wu, Y., Zhu, X., Chen, J. and Zhang, X. (2013), EINVis: A Visualization Tool for Analyzing and Exploring Genetic Interactions in Large-Scale Association Studies. Genet. Epidemiol., 37: 675–685. doi: 10.1002/gepi.21754
- Issue published online: 15 OCT 2013
- Article first published online: 11 AUG 2013
- Manuscript Accepted: 11 JUL 2013
- Manuscript Revised: 24 JUN 2013
- Manuscript Received: 28 MAR 2013
- US National Science Foundation. Grant Numbers: IIS-1162374, IIS-1218036, DBI-1062057, IIS-1302755, EPS-0903234, DUE-0817106
- Public Health Service. Grant Number: HG003054
- US National Human Genome Research Institute
- gene-gene interaction;
Epistasis (gene-gene interaction) detection in large-scale genetic association studies has recently drawn extensive research interests as many complex traits are likely caused by the joint effect of multiple genetic factors. The large number of possible interactions poses both statistical and computational challenges. A variety of approaches have been developed to address the analytical challenges in epistatic interaction detection. These methods usually output the identified genetic interactions and store them in flat file formats. It is highly desirable to develop an effective visualization tool to further investigate the detected interactions and unravel hidden interaction patterns. We have developed EINVis, a novel visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. It utilizes a circular layout (specially, a tree ring view) to simultaneously visualize the hierarchical interactions between single nucleotide polymorphisms (SNPs), genes, and chromosomes, and the network structure formed by these interactions. Using EINVis, the user can distinguish marginal effects from interactions, track interactions involving more than two markers, visualize interactions at different levels, and detect proxy SNPs based on linkage disequilibrium. EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions. It is publicly available with detailed documentation and online tutorial on the web at http://filer.case.edu/yxw407/einvis/.