Introduction

SCAD-Brain, a web-based platform and database for single cell RNA-seq (scRNA-Seq) data from Alzheimer's disease (AD) brain tissues.

Single-cell RNA sequencing (scRNA-seq) is extremely effective in interpreting the cellular heterogeneity of AD. With the development of scRNA-Seq technologies, a large amount of scRNA-seq data has been generated. Analyses of gene expression, cell communication, and cell trajectories of AD using scRNA-Seq are urgent needed to facilitate the understanding of the pathogenesis, cellular heterogeneity, and cell development of AD.

Here, we provided SCAD-Brain, which provides single-cell expression/interaction/trajectory profile that covering 17 scRNA-Seq projects, 21 datasets, 359 samples, 10 Brain regions, 16 cell types and their subtypes, and 1,564,825 cells. Based on these data, SCAD-Brain provides five modules:1) Cell markers, 2) Comparison between cell types, 3) DEGs between AD and normal (or between Braak stages), 4) Cell communication, and 5) Cell trajectory.

These modules performs:

Cell markers: Summary the marker genes, proportions, and biological pathways of each cell type.

Comparison between cell types: Differentially expressed genes (DEGs) between two cell types, and their enriched KEGG and GO pathways.

DEGs between AD and normal: DEG between AD and Control, between AD and MCI, and between Braak staging groups, and their enriched KEGG and GO pathways.

Cell communication: Predicts and visualizes the ligand-receptor pairs that communicate cells.

Cell trajectory: Model the dynamic processes of cell differentiation and development trajectory.

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Cell markers analysis

The 'Cell markers' module analyzes the expression of cell markers in each cell type. The module provides functions including cell annotation, marker genes’ expression visualization, and pathway enrichment analysis.

Please select one dataset:

Cell annotation and cell proportion of the selected data set.

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Introduction

Cell markers analysis

Cell annotation:

Cell annotation for the selected dataset

Proportion of cell types:

The proportion of cell types in each sample of selected dataset

Comparison between one cell type and others

Figure 1:

Top 20 cell markers of the selected cell type filtered by the avg_log2FC absolute value

Figure 2:

Top 20 cell markers of the selected cell type filtered by the pct.1-pct.2 absolute value

KEGG pathways enriched in up-regulated cell markers in selected cell type

KEGG pathways enriched in down-regulated cell markers in selected cell type

Figure 1:

The enriched KEGG pathways of up-regulated cell markers in the selected cell type

Figure 2:

The enriched KEGG pathways of up-regulated cell markers in the selected cell type

Figure 3:

The enriched KEGG pathways of down-regulated cell markers in the selected cell type

Figure 4:

The enriched KEGG pathways of down-regulated cell markers in the selected cell type

GO-BP (Biological processes) pathways enriched in up-regulated cell markers in selected cell type

GO-BP (Biological processes) pathways enriched in down-regulated cell markers in selected cell type

Figure 1:

The enriched GO-BP pathways of up-regulated cell markers in the selected cell type

Figure 2:

The enriched GO-BP pathways of up-regulated cell markers in the selected cell type

Figure 3:

The enriched GO-BP pathways of down-regulated cell markers in the selected cell type

Figure 4:

The enriched GO-BP pathways of down-regulated cell markers in the selected cell type

GO-MF (Molecular function) pathways enriched in up-regulated cell markers in selected cell type

GO-MF (Molecular function) pathways enriched in down-regulated cell markers in selected cell type

Figure 1:

The enriched GO-MF pathways of up-regulated cell markers in the selected cell type

Figure 2:

The enriched GO-MF pathways of up-regulated cell markers in the selected cell type

Figure 3:

The enriched GO-MF pathways of down-regulated cell markers in the selected cell type

Figure 4:

The enriched GO-MF pathways of down-regulated cell markers in the selected cell type

GO-CC (Cellular component) pathways enriched in up-regulated cell markers in selected cell type

GO-CC (Cellular component) pathways enriched in down-regulated cell markers in selected cell type

Figure 1:

The enriched GO-CC pathways of up-regulated cell markers in the selected cell type

Figure 2:

The enriched GO-CC pathways of up-regulated cell markers in the selected cell type

Figure 3:

The enriched GO-CC pathways of down-regulated cell markers in the selected cell type

Figure 4:

The enriched GO-CC pathways of down-regulated cell markers in the selected cell type

Comparison between cell types

Comparison between one cell type and another

Figure 1:

Top 20 DEGs of the selected cell types filtered by the avg_log2FC absolute value

Figure 2:

Top 20 DEGs of the selected cell types filtered by the Pct.1-Pct.2 absolute value

KEGG pathway enrichment of DEGs between selected two cell types

Figure 1:

The enriched KEGG pathways of DEGs between selected two cell types

GO enrichment of DEGs between selected two cell types

Figure 1:

The enriched GO-BP pathways of DEGs between selected two cell types

Figure 2:

The enriched GO-MF pathways of DEGs between selected two cell types

Figure 3:

The enriched GO-CC pathways of DEGs between selected two cell types

AD vs control

DEGs of each cell type between AD and control

Figure 1:

DEGs of selected cell type between AD and control

Figure 2:

The Z-score of top 20 DEGs’ expression in each cell type in AD and control groups

KEGG pathway enrichment of DEGs of selected cell type between AD and control

Figure 1:

The enriched KEGG pathways of DEGs of selected cell type between AD and control

GO pathway enrichment of DEGs of selected cell type between AD and control

Figure 1:

The enriched GO-BP pathways of DEGs of selected cell type between AD and control