Additional file 2: of A simulation study investigating power estimates in phenome-wide association studies

Summary Results: The summary results used to generate the figures. (XLSX 56 kb

Additional file 1: of A simulation study investigating power estimates in phenome-wide association studies

Figure S1. Binary Trait Type I Errors. The plot shows the Type I errors for different parameter settings. Each panel represents the different case number on the top and case-control ratio on the right which was used for the simulation dataset. The Type I error on the y-axis is calculated based on the number of false positive association below significance level of α = 0.00025. The disease penetrance is represented on the x-axis and each colored point represent different MAF used in the simulations. (PNG 379 kb

Flow chart explaining all the steps for gene based interaction analysis in discovery (eMERGE) and replication dataset (NEIGHBOR).

<p>Flow chart explaining all the steps for gene based interaction analysis in discovery (eMERGE) and replication dataset (NEIGHBOR).</p

Principal component analysis (PCA) of 5090 samples (glaucoma cases and controls) from eMERGE network.

<p>Eigenvector 1 is on x-axis and eigenvector 2 is on y-axis. Each point is a sample and they are color coded by case and control status.</p

Circular plot representing only unique gene-gene interactions.

<p>Genes are colored as red if they are expressed in eye and as grey if not expressed in the eye. All genes are ordered by chromosome. Links between the genes represent gene-gene interactions that are replicated.</p

POAG GWAS Results in eMERGE dataset.

<p><b>(A)</b> Manhattan plot shows chromosome and base pair positions on x-axis and -log10 of p-value on y-axis. Each point here represents a SNP. Red line is the genome-wide significance line at 5e-08. Highlighted points indicate annotation of SNPs with previously reported GWAS associated genes. <b>(B)</b> Shows a QQ-plot from GWAS analysis.</p

Heat map representing expression of the unique genes found in the ocular tissue database from GXG interaction results.

<p>Here, the x-axis lists all genes and y-axis lists the names of 10 tissues from the eye. Scale and color intensity represent PLIER values as reported in the ocular tissue database.</p

Hierarchal plot showing 16 genes in red circles and 11 pathways in blue rectangles.

<p>Connection between the genes and pathways was established using Biofilter 2.0.</p

Synthesis view plot representing unique gene-gene interaction models and their p-values in discovery and replication dataset.

<p>Synthesis view plot representing unique gene-gene interaction models and their p-values in discovery and replication dataset.</p

All replicating gene-gene interactions at LRT p-value <1e-04 for replication dataset.

<p>All replicating gene-gene interactions at LRT p-value <1e-04 for replication dataset.</p