Fig. 5: The structural changes of the co-expressed proteins by WGCNA.

A Four of the seven tissues (brain, kidney, muscle and spleen) showed significant correlated modules (R² > 0.4, Two-sided Student’s t-test, P-value < 0.05). B In module 3 (M3) of brain, the eigenprotein level between AD and NC was assessed, with dot colors indicating the age of the mice. Three mice per age were used for both NC and AD. The minima/maxima are the lowest/highest data point. Center line denotes median, box edges indicate the 25th and 75th percentiles, and whiskers extend to ±1.5 interquartile range (IQR). C–E The labeled peptides of M3 proteins were clustered based on the fold-change of the accessibility (C). Distribution of the fold-change of the accessibility of cluster 1 (D) and cluster 2 (E). Of 481 labeled peptides that mapped onto 174 proteins in M3, fold-change of accessibility of 268 peptides showed a consistent decrease in progressing AD in cluster 1 and fold-change of accessibility of 213 peptides in cluster 2 did not significantly change in progressing AD. P-values from two-sided Student’s t-test are shown between the indicated groups. F–I The fold changes of the accessibility for Map1a (F), Psat (G), Mag (H), and Plp1 (I) are presented. The peptides in the bold box were included in cluster 1. Peptides in the bold box clearly decreased. Source data are provided as a Source Data file.