GEGEINTOOL: A Computer-Based Tool for Automated Analysis of Gene-Gene Interactions in Large Epidemiological Studies in Cardiovascular Genomics

摘要

Current methods of data analysis of gene-gene interactions in complex diseases, after taking into account environmental factors using traditional approaches, are inefficient. High-throughput methods of analysis in large scale studies including thousands of subjects and hundreds of SNPs should be implemented. We developed an integrative computer tool, GEGEINTOOL (GEne-GEne INTeraction tOOL), for large-scale analysis of gene-gene interactions, in human studies of complex diseases including a large number of subjects, SNPs, as well as environmental factors. That resource uses standard statistical packages (SPSS, etc.) to build and fit the gene-gene interaction models by means of syntax scripts in predicting one or more continuous or dichotomic phenotypes. Codominant, dominant and recessive genetic interaction models including control for covariates are automatically created for each SNP in order to test the best model. From the standard outputs, GEGEINTOOL extracts a selected set of parameters (regression coefficients, p-values, adjusted means, etc.), and groups them in a single MS Excel Spreadsheet. The tool allows editing the set of filter parameters, filtering the selected results depending on p-values, as well as plotting the selected gene-gene interactions to check consistency. In conclusion, GEGEINTOOL is a useful and friendly tool for exploring and identifying gene-gene interactions in complex diseases.