Supplementary Figure 5: Module preservation between iMN and sALS data sets (see Figs. 2 and 5).
From: ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks
(a) Measure of how well 55 modules defined in the iMN data set are preserved in the sALS data set. The Z-summary statistic (y-axis) for is plotted against module size (x-axis). Data points reflect module color. Dashed green line indicate threshold at Z = 10, and dashed blue line indicate threshold at Z = 2. For the likelihood of module preservation, Z-summary > 10 indicates strong evidence; 10 > Z-summary > 2 indicates moderate to weak evidence, and 2 > Z-summary indicates no evidence. (b) Measure of how well 55 modules defined in the iMN data set are preserved in the sALS data set, as a relative comparison among modules. The median rank statistic (y-axis) is plotted against module size (x-axis). Data points reflect module color. Low median rank values indicate a high preservation. (c) As in a, except applied to 52 modules defined in the sALS data set and tested for preservation in the iMN data set. (d) As in b, except applied to 52 modules defined in the sALS data set and tested for preservation in the iMN data set. (e) Pathogenic ALS genetic variants have higher intramodule membership than genes not affect by variants. Among the 4,711 genes classified into modules, genes were divided by either those affect by pathogenic variants versus unaffected genes for either motor neuron disease (first and second bins, respectively with n = 139 and n = 4,572) or ALS (third and fourth bins, respectively with n = 67 and n = 4,644). Significance was tested using the Wilcoxon rank-sum test. For MN, W = 339,949, for ALS, W = 182,087, and P-values are indicated above comparisons. The median intramodule membership of MN disease variants is higher than unaffected genes, but not significantly. The ALS variants have a significantly higher intramodule membership than unaffected genes. For additional information, see Supplementary Tables 2c (for iMN module assignments and properties), 5c (for sALS module assignments and properties), and 5d (for module preservation statistics).
