Figure 1 (top panel) presents a Phenotype-Genotype Association (PGA) grid for a single SNP. Color coding denotes levels of statistical significance. In this example, associations having nominal P-values
The PGA grid is interactive. Clicking on a specific cell generates a plot of adjusted least squares means for the trait of interest by genotype for the corresponding genetic model. Figure 1 (bottom panel) displays this plot for the highlighted cell in Figure 1 (LV fractional shortening for pooled sexes, general model, adjusted for age and sex). At the gene level, thumbnail PGA grids for each typed SNP are displayed on a single page with each thumbnail sorted by map position and hyperlinked to its full-sized parent grid. The underlying database can be searched by gene, P-value, or phenotype to facilitate hypothesis generation and pursuit [4].
The software to create PGA grids from user-supplied data (sample sizes, means and standard errors, P-value for association) utilizes a database-backed web server. We generate HTML pages using Tcl scripts on an AOLserver platform [5] using an Oracle database [6], and the ArsDigita Community System web toolkit [7]. Source code (see Additional Files 1 and 2, available upon request) is available for free download [8]and can be adapted for use elsewhere on other database-backed web platforms. The grid can be modified to display results for gene-environment interactions (Figure 2). In addition the grid can used to summarize analyses of qualitative traits or haplotypes [3]. For example, one could display a grid for each gene with cells to indicate block-specific P-values based on a global test of differences in phenotype across all haplotypes within the block (Figure 3).
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