Fig. 5: PUMICE+ identifies the largest number of gene x trait associations and novel associations across 48 GTEx tissues using GWAS summary-level statistics of 79 traits. | Nature Communications

Fig. 5: PUMICE+ identifies the largest number of gene x trait associations and novel associations across 48 GTEx tissues using GWAS summary-level statistics of 79 traits.

From: Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies

Fig. 5

Panel (a) displays the total number of significant gene x trait associations by each method. Panel (b) shows the number of unique significant gene x trait associations. Gene x trait associations identified in multiple tissues are counted only once. Panel (c) shows the number of independent gene counts. Multiple significant genes within 1 Mb window are counted only once. Panel (d) shows the number of independent novel genes that are outside 1 Mb window on either side of GWAS sentinel variant. PUMICE+ identifies the highest number of gene x trait associations, unique gene count, independent gene count, and novel gene count in comparison to all other methods. Panel (e) displays the distribution of chi-square test statistics at MAGMA-prioritized genes. Median value is denoted in the parentheses. PUMICE+ achieved the largest median value of chi-square values (22.45). P-value is based on the comparison between PUMICE+ and other method using one-sided median test. *** denotes significant differences with p < 0.001. One-sided p-values are provided in the source data file. Each boxplot is derived from the chi-square values across 12,546 MAGMA-prioritized genes. Minima and maxima values (excluding outliers) are represented by the lower- and upper-bound of the whiskers. Median value is represented by the bold line in the middle. First and third quartiles are represented by the lower- and upper-bound of the box.

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