GAIN is based on interaction information between three attributes; in this case, between two single nucleotide polymporphisms (SNPs) and a class or phenotype attribute. Interaction information is the gain in phenotype information obtained by considering SNP A and SNP B jointly beyond the phenotype information that would be gained by considering SNPs A and B independently.

Thus, each edge in a GAIN represents the increase in information about the phenotype achieved by considering the two SNPs jointly compared to the expected increase in information with the assumption of independence between the SNPs. We emphasize that a connection between SNPs in a GAIN is specific to the given phenotype because it measures the correlation between two SNPs that influences association with the phenotype. The network can be exported to Cytoscape or visualized interactively within the GAIN tool.

Tutorial

Requirements

Java

References

B.A. McKinney, J.E. Crowe, Jr., J. Guo, and D. Tian, "Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis," 2009, PLoS Genetics 2009, 5(3): e1000432. doi:10.1371/journal.pgen.1000432. open source

Acknowledgments

We would like to acknowledge the developers of prefuse.

Send inquiries to brett.mckinney@gmail.com.

http://sites.google.com/site/mckinneylab/software/'>McKinneyLab