Average gene expression. Heatmap of gene expression (rows), averaged across individuals, in each unique combination of cell type and region (columns).
Pseudobulk gene expression Heatmap or violin plots of gene expression (rows), averaged across cells in each unique combination of celltype and sample. Samples collected in each brain region from each individual.
UMAP representation of cells: Cells labeled by cell type (left). Cells labeled by metadata attribute (dropdown) (right).
Module comparison: Violin plots (single module) or scatterplots (module-module) of module scores. Modules scores are reported at sample level for module comparisons across cell type groups or at the sample + subtype level for comparisons within a group. Tables (right) give correlations of module 1's score against other modules and metadata covariates.
Table of DEG status for genes in modules. Download Full Table (TSV)
Barplot of DEG status (up/down) for genes in modules.
Module scores (pseudobulk). Heatmap or violin plots of scores at the pseudobulk level (cell type + sample). Module scores are z-scored by default. Modules for first selected cell group are shown.

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Resources

Supplementary tables
  1. Table in xlsx - Gene expression marker lists
  2. Table in xlsx - Gene expression programs from cNMF
  3. Table in xlsx - Transcriptional regulons from SCENIC
  4. Table in xlsx - Modules and module scores for GABAergic, glutamatergic, and projecting neurons
  5. Tables in xlsx, Rds - Gene expression modules from scmodule
  6. Table in xlsx, tsv - Gene expression module covariate enrichments
  7. Tarball of tables tar.gz - Differential gene expression tables
  8. Table in tsv - Genes associated with subtype resilience and vulnerability
Modules resources:

Modules resources (genes/expression profiles/associations) are downloadable from this directory.