APOE-4 Risk Factor & Alzheimer's Disease
Multi-Dataset Research Database
An integrated platform for exploring transcriptomic changes across human iPSC-derived brain cells, post-mortem brain tissue, and the Seattle Alzheimer's Disease Brain Cell Atlas — stratified by APOE genotype and disease severity.
iPSC Brain Cells
Gene expression from CRISPR-edited human iPSC-derived astrocytes, microglia, and mixed cortical cultures. Isogenic APOE33 vs. APOE44.
Human Post-Mortem Brain
RNA-Seq from MSBB (4 cortical regions) and ROSMAP (DLPFC). Stratified by APOE haplotype and AD severity via CERAD, PlaqueMean, Braak, CDR.
Seattle AD Brain Cell Atlas
Allen Institute's single-cell atlas of the human Alzheimer's disease brain. Cell-type–specific transcriptional signatures and pathway enrichment.
iPSC-Derived Brain Cells
Single-cell Expression Explorer
Select a gene and click Plot to visualize UMAP cell embeddings and gene expression.
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BF768 Spring 2026 · Team 14
Wendy Bui · Chloe Ploss · Vaidehi Gupta · Mildred Monsivais
Multi-Gene Expression
Compare expression patterns across multiple genes using dot plots (size = % expressing, color = avg log-normalized expression) or clustered heatmaps.
Loading data…Cell Type Composition
Sample-level cell type proportions stratified by APOE genotype. Relative abundance of astrocytes, microglia, neurons, and other populations per sample.
Loading data…Post-Mortem Brain RNA-Seq
Seattle Alzheimer's Disease Brain Cell Atlas (SEAAD)
Help & User Guide
How to use the scRNA-seq Explorer and all interactive features
Getting Started
Use the top navigation tabs to switch between datasets (iPSC, Post-Mortem, SEAAD). Within iPSC, toggle between Bulk and Single-Cell using the buttons in the header, then select a sub-tab (Single-cell Expression, Multi-Gene Expression, Cell Type Composition, Data Table).
Input Format
Gene inputs should use official HGNC gene symbols, such as APOE, GFAP, or MAPT. The search box auto-completes from the full ~19,000 gene list — type at least 2 characters, then press Enter or click a suggestion to confirm. For multi-gene plots, add up to 10 genes using the search box in the Multi-Gene tab. Filters are optional; leaving them on "All" includes all available data.
Single-cell Expression
Enter a gene symbol, select your APOE Genotype option (APOE 33, APOE 44, Merged, or All 3 panels), apply any cell type or sample filters, then click ▶ Plot. The top panels show cell-type UMAP embeddings (color = cell identity); the bottom panels show gene expression on the same UMAP (color intensity = log-normalized expression). Color scale: purple for merged, blue for APOE 33, red for APOE 44. Use the Display Options radio to switch the bottom panels between Gene Expression UMAP, Violin Plot, or Dot Plot.
Multi-Gene Expression
Add genes using the search box (up to 10). Select a genotype and cell type filter. Choose Dot Plot (dot size = % of cells expressing the gene; color = average log-normalized expression) or Heatmap (rows = genes, columns = cell types; color = mean expression). Click ▶ Plot.
Cell Type Composition
Select your APOE Genotype option, cell type, and sample filters. Choose Stacked Bar (each bar is one sample; segments show proportions of each cell type) or Box Plot (distribution of cell-type proportions across samples). The Merged panel combines APOE 33 and APOE 44 samples; individual panels show genotype-specific views. Click ▶ Plot.
Data Table
Select a gene, choose a genotype option, and apply cell type, sample, and minimum expression filters. Set a Row Limit (default 500) to control how many rows are returned, then click ▶ Query. Results are sorted by expression (highest first). Use ↓ Download CSV to export the table.
Interactive Plot Controls
Hover over any data point to see gene expression values, cell type labels, genotype, and sample metadata. Click legend items to hide or show specific groups. The Plotly toolbar appears on hover (top-right of each plot) and provides: zoom, pan, reset axes, and download plot as PNG. Use the camera icon in the toolbar to save a high-resolution image of any individual plot.
Bulk Sub-tabs (Normalized Counts, Pathway Barplot, Heatmap)
These tabs display George's interactive Shiny-style HTML files embedded as iframes. Use the controls within each panel (dropdowns, gene search, buttons) to filter and update the visualizations. These do not require clicking a Plot button — they update interactively within the iframe.