Fig. 4

Differentially expressed genes (DEGs), Top-20 enriched pathways and layer-specific DEGs in AD vs CT human MTG. (A) The Fisher’s exact test between DEGs (AD vs CT 1008 upregulated) identified in our study and 14 previously published AD-related transcriptomic and proteomics datasets (Additional file 7: Table S6). The x-axis and y-axis indicate objects of Fisher’s exact test. Heatmap block color indicates the log-transformed odds ratio. Each heatmap block is labeled by its adjusted p-value. If the heatmap block has a non-significant adjusted p-value, the block color was assigned as white. WAM, WM-associated microglia; PIG, plaque-induced gene; OLIG, oligodendrocyte gene; DAM, disease-associated microglia; ARM, amyloid-response microglia; A1, A1 astrocytes. (B) Gene Ontology (GO) pathway analysis of DEGs between AD and CT cases. DEGs were assessed with the Seurat FindMarkers function with a log-fold-change threshold of 0.25. Bonferroni-adjusted p-values were used to determine significance at an FDR < 0.05. Dot plot shows the top 20 enriched GO terms which represent biological process terms from the DEGs between AD and CT. Each dot is colored by the Benjamini–Hochberg adjusted p-value. The dot size is scaled by the number of overlapping genes with the related GO terms. The x-axis is scaled by the ratio between the overlapping count and the total number of genes of the term. Gene set enrichment analysis was performed using the Enrichr web server. (C) Heatmaps of Z-scores for layer-specific upregulated DEGs identified between AD and CT cases. The heatmaps show the expression levels of layer-specific DEGs in each layer for each AD and CT case. Layer I of AD-2 is shown in gray since this layer was not present in our sampled brain block. The red color indicates a relevantly higher expression than other cases, while the blue color indicates a lower expression