Fig. 5

TMT-LysC AD Protein Network Summary. The overlap of proteins within each TMT-LysC module with cell type specific protein markers from microglia, astrocytes, oligodendrocytes (oligo), and neurons is shown by single color heat map (increased red represents increased overlap). Correlation between module eigenprotein and neuritic amyloid plaque burden (CERAD score), tau tangle burden (Braak stage), Aβ17–28, phosphorylated tau pT231 peptide (VAVVRpTPPKSPSSAK), U1-70K small nuclear ribonucleoprotein, TAR DNA-binding protein 43 (TDP-43), and last mini-mental state examination (MMSE) score prior to death, is shown by two-color heat map (red represents positive correlation, blue represents negative correlation). The overlap of alt-EEjxns and different classes of RNA binding proteins is shown by single color heat map. A, McKnight 570 refers to RNA binding proteins that are often found within RNA granules as described in [48]; B, Total Observed RNA binding refers to all RNA binding proteins commonly observed in our proteomic experiments; C, proteins that interact with the low complexity 2 (LC2) domain of the U1-70K small nuclear ribonucleoprotein 70 kDa (snRNP70) [54]; D, proteins that are homologous to U1-70K; E, proteins that interact with the LC1 or basic-acidic dipeptide (BAD) repeat domain of U1-70K [54]; F, low complexity arginine-serine (RS) repeat-containing proteins; G, proteins annotated as comprising the spliceosome complex in the Kyoto Encyclopedia of Genes and Genomes (KEGG); H, proteins annotated as involved in RNA translation by Gene Ontology (GO); I, proteins annotated in KEGG as belonging to the U1 spliceosome complex. Overlap was calculated by Fisher exact test. P values are corrected by Benjamini-Hochberg FDR. Bicorrelation was performed for CERAD, Braak, and molecular species. Spearman correlation was performed for MMSE. Detailed data for all correlations are provided in Supplementary Data