Fig. 2.

Association of pathogenic and population missense variations with 40 3D features (a combination of structural, physicochemical, and functional features of amino acids on protein structure) for 1,330 disease-associated genes (DAGS1330 set). The plot shows the results of two-sided Fisher’s exact tests of association between 32,923 pathogenic and 164,915 population amino acid variations with the features. Circles show the OR and are labeled with the $q$ values (the corrected $p$ values; see Materials and Methods), showing the significance of the association (a value of 1.0e-297 should be read as $<$1.0e-297, indicating the maximum significance), and the horizontal bars show the 95% CI. The OR > 1 and OR < 1, along with $q\hspace{0.17em}<$ 0.05, indicate that the corresponding feature (y axis) is enriched in pathogenic (red circle) and population (blue circle) variants, respectively. The vertical dashed line at OR = 1 indicates no association between a variant type (pathogenic or population) and a feature. To facilitate the visualization, minimum and maximum values of OR along the x axis are set to 0.2 and 20.0, respectively. For nonsignificant association ($q\hspace{0.17em}\ge$ 0.05), the circle, CI bar, and feature names are gray.