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Bioinformatics Advance Access originally published online on October 10, 2006
Bioinformatics 2007 23(2):249-251; doi:10.1093/bioinformatics/btl510
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

KGraph: a system for visualizing and evaluating complex genetic associations

Reagan J. Kelly 1,2,*, Douglas M. Jacobsen 1, Yan V. Sun 1, Jennifer A. Smith 1 and Sharon L. R. Kardia 1,2

1 Department of Epidemiology, School of Public Health, University of Michigan Ann Arbor, MI 48104, USA
2 Bioinfromatics Program, University of Michigan School of Medicine Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The KGraph is a data visualization system that has been developed to display the complex relationships between the univariate and bivariate associations among an outcome of interest, a set of covariates, and a set of genetic factors, such as single nucleotide polymorphisms (SNPs). It allows for easy viewing and interpretation of genetic associations, correlations among covariates and SNPs, and information about the replication and cross-validation of the associations. The KGraph allows the user to more easily investigate multicollinearity and confounding through visualization of the multidimensional correlation structure underlying genetic associations. It emphasizes gene–environment and gene–gene interaction, both important components of any genetic system that are often overlooked in association frameworks.

Availability: http://www.epidkardia.sph.umich.edu/software/kgrapher

Contact: reagank{at}umich.edu

Supplementary information: A description of system requirements and a full user manual are available at http://www.epidkardia.sph.umich.edu/software/kgrapher

Associate Editor: Keith A Crandall

Received on August 15, 2006; accepted on September 30, 2006

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