Fig. 2: Overview of ssREAD functions.
From: A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)
a Features and visual representations related to sc/snRNA-seq, encompassing cell type annotations, marker gene expressions, and graphic depictions via bar and violin plots. Each box showcases the minimum, first quartile, median, third quartile, and maximum average expression values of a cell type (Ast: n = 208, Endo: n = 28, EN: n = 2,696, IN: n = 740, MIC: n = 266, OPC: n = 195, and Olig: n = 1,546). Dots represent outliers. b Functions and visualizations pertinent to ST, highlighting H&E imagery, layer annotations, marker gene expressions, and spot deconvolutions. c DEG analysis, with comparisons drawn between categories like Cell Type 1 vs. Cell Type 2 (CT1 vs. CT2), AD vs. Control, Male vs. Female, Brain Regions 1 vs. 2, etc. p-values were calculated based on two-sided Wilcoxon Rank–sum test and adjusted using Bonferroni correction. d Functional enrichment analysis focusing on GO ontology and KEGG pathways. p-values were calculated using the Hypergeometric test from Enrichr and were adjusted using the Benjamini–Hochberg correction method. e Predictions of cell type-specific regulons. The following abbreviations are used for cell types: Ast astrocytes, Endo endothelial cells, EN excitatory neurons, IN inhibitory neurons, Mic microglia, Olig Oligodendrocytes, OPC oligodendrocyte precursor cells.
