Integrated protein co‐expression and differential expression across the ALS‐FTD disease continuum Integrated protein co‐expression and differential expression across the ALS‐FTD disease continuum Eigenproteins, which correspond to the first principal component of a given module and serve as a summary expression profile for all proteins within a module, are shown for 10 of the 15 modules generated by WGCNA. Box plots depict mean (horizontal bars) and variance (25th to 75th percentiles), with whiskers extending to the last non‐outlier measurements, are shown for all four groups (control, ALS, ALS/FTD, and FTD), and representative Gene Ontology (GO) terms are listed above each eigenprotein. Hub proteins for each of these modules are also highlighted. Significance was determined by comparisons of quantified proteins within individual cases across the clinical groups to the module eigenprotein using one‐way nonparametric ANOVA Kruskal–Wallis with P‐values listed above plots. Outlier cases are shown as open circles beyond the error bars.Stacked bar plots represent analysis of differential expression (pairwise comparison between disease group and control) and enrichment of differentially expressed proteins within co‐expression modules. Modules are listed along the x‐axis, and the height of the bar along the y‐axis indicates the proportion of differentially expressed module members, while the color indicates the fold change (red is increased, and blue is decreased) according to the scale shown. Mfon E Umoh et al. EMBO Mol Med. 2017;emmm.201708202 © as stated in the article, figure or figure legend