BrainScope

BrainScope visualizes spatial and temporal human brain transcriptomics data from the Allen Atlases to enable exploration of gene expression patterns across brain regions, the genome, and developmental stages.

Key Features:

• Dual t-SNE Methodology: Employs dual t-distributed Stochastic Neighbor Embedding (dual t-SNE) to generate linked visualizations of both genes and samples for high-dimensional transcriptomics data across the whole brain, genome, and developmental stages.
• Spatial and Temporal Visualization: Integrates spatial mapping of gene expression across anatomical brain regions with temporal profiling across developmental stages.
• Gene Co-expression Modules: Identifies and visualizes gene co-expression modules that are significantly enriched for specific biological functions.
• Region-Specific Gene Functions: Maps t-SNE topography to highlight region-specific gene functions and the topographic organization of the transcriptome.

Scientific Applications:

• Cell Type Specific Gene Analysis: Analyzes gene sets specific to various brain cell types to characterize cellular functions and interactions.
• Stable Gene Co-expression Modules: Examines stable gene co-expression modules across adult human donors for comparative studies and identification of conserved genetic patterns.
• Developmental Evolution Analysis: Studies how gene co-expression evolves over developmental stages, including analyses focused on oligodendrocyte-specific genes.

Methodology:

Uses dual t-distributed Stochastic Neighbor Embedding (dual t-SNE) for dimensionality reduction and linked visualization of genes and samples, aligning spatial samples with anatomical regions and mapping gene densities to co-expression modules.