Fig. 6

Modules and subnetworks of co-regulated proteins that are dysregulated in FTLD-tau and FTLD-TDP. A–D Density curves of the log2 fold change (log2FC) values of all the proteins belonging to a module in the discovery data set and the validation data set. The p-value indicates the significance of the median log2FC difference compared to NHC. E–H Permutation test to validate the differential abundance of modules identified in the discovery data set. The y-axis shows the fraction of proteins where the log2FC measured in the validation data set was in the same direction as in the discovery data set, and the p-value was below the threshold (x-axis) in both the discovery and validation data set (blue line). We used a permutation test, where we repeated this procedure with the protein labels in the validation data set randomly reassigned 1000× (grey lines). The module was considered validated if the average p-value at thresholds 0.1, 0.5, 0.5, and 0.8 was lower than 0.05 (GESS score). Fraction validated: fraction of the proteins in the module that have a log2FC in the same direction as in the discovery data set. I–L Subnetworks of most highly and significantly dysregulated proteins within the corresponding module of co-regulated proteins in the discovery data set. Red nodes indicate a positive log2FC, and blue nodes indicate a negative log2FC. The darkness of the borders reflects the significance. M–P Subnetworks of most highly and significantly dysregulated proteins in the validation data set. Red nodes indicate a positive log2FC, and blue nodes indicate a negative log2FC. The darkness of the borders reflects the significance