🧠 brain-development browser

A uniformly processed atlas of human brain development defines cell type-specific maturation trajectories across lifespan

How to explore the data

UMAP markers : Compare the aggregate expression of cell type markers on the UMAP besides individual marker gene expression.
Maturation trajectory : Visualize how transcriptionally similar a cell type is to its adult counterpart at each developmental stage; Plots show MetaNeighbor AUROC scores for each cell type vs age. Values rising toward 1.0 indicate convergence on the adult state.
Gene importance & trajectories : Examine top genes predictive of cell type maturation by plotting gene importance scores and visualize expression trajectories across the entire developmental span for all genes.
Developmental metamodules : Developmental metamodules are co-regulated gene sets derived from first trimester and mid-gestation brain samples. Explore module expression in different cell types and gene ontology enrichment. Pick a module to see its top enriched GO BP terms and to inspect specific genes in the next tab.
Module browser & gene pair coexpression : Explore module gene membership and coexpression over age, and visualize coexpression of any gene pair within and across celltypes at different timepoints.

Tip: Some visualizations may take time to load, particularly the within and cross-celltype coexpression for a gene pair.

Contact: © Sridevi Venkatesan — sridevivenkatesan.uoft@gmail.com

Instructions

Select a cell type and a marker gene to visualize the aggregate expression of cell type markers and beside the individual marker gene expression on the UMAP.

Aggregate marker set expression

Selected marker gene expression

Cell type

Marker gene

Left: aggregate marker expression for the selected cell type. Right: UMAP for the chosen marker gene.

Instructions

Select a cell type to visualize its transcriptional similarity to its adult counterpart at each developmental stage; Plots show MetaNeighbor AUROC scores for each cell type vs age. Values rising toward 1.0 indicate convergence on the adult state. Dotted lines denote birth.

Instructions

To examine the importance of a gene in predicting maturation of a cell type, select a gene on the left. Gene importance scores indicate the frequency of gene usage across bootstrap age-prediction models. To plot a gene's expression over age, go to the expression over age tab. Dotted lines denote birth

Gene importance
Expression over age

Cell-type legend groupings

Progenitor: Neural Progenitor, Dividing Progenitor, Intermediate Progenitor
Early cells: Newborn neurons, Cajal Retzius, Newborn non-neurons, fetal microglia/immune
Glutamatergic non-IT: L6b, L6 CT, L5/6 NP, L5 ET
Glutamatergic IT: L6 IT — L2/3 IT
GABAergic MGE: Pvalb, Sst, Sst Chodl
GABAergic CGE: Vip, Pax6, Sncg, Lamp5, Lamp5 Lhx6 (Lamp5 Lhx6 are MGE-derived, but grouped here due to their similarity to Lamp5)
Glia: Astro, OPC, Oligo
Non-neuron: Endo, VLMC, Micro/PVM

Instructions

Developmental metamodules are derived from 1st trimester and mid-gestation samples. The heatmap below shows module expression per cell type for the selected age. Use the sidebar to pick a module and age — the chosen module is marked with a black tick on the top bar. The module's top enriched GO terms will be shown below the heatmap. You can also explore this module's genes in more detail by clicking the button on the bottom left.

Module x cell-type heatmap

GO BP enrichment (top terms for selected module)

Module set

<14gw 20-25gw

Age window

Trimester 1 Trimester 2 Trimester 3 Postnatal

Module to inspect

Type or pick a module ID above. The selected module is marked with a black tick on the top of the heatmap, and its top GO BP terms appear below.

Instructions

Explore module gene membership and co-expression over age, and plot co-expression of any gene pair within and across cell types at different timepoints. You can select modules by module number or their genes. The tab coexpression x age displays selected modules' co-expression within and across cell types over age. A gene pair from the chosen module is pre-selected or you can pick any two genes to visualize their coexpression within and across cell types at a selected age. This may take a few seconds to load up.

Module table (click rows to select)

Module coexpression x age

Within-celltype coexpression Download PDF

Across-celltype coexpression + expression by celltype Download PDF

Modules

Module set

<14gw 20-25gw

Filter modules by module ID or gene (optional)

Click a row to pick that module; the gene-pair selectors below auto-fill with the first two genes.

Gene-pair coexpression

Age window

Gene A

Gene B

Pick both genes from the same module above for coherent pairs; any pair is allowed.

Contact

Reach out if you have any questions:

This work was done through the BICAN developmental integrative analysis working group . For more information about BICAN, visit brain-bican.org .