Getting Started: Gene Expression Heatmap

The Heatmap visualization shows a heatmap of gene expression across the taxonomy of Cell Types for the current dataset. The default genes displayed provide waypoints across the taxonomy as a whole. The colors depict the average expression value (either median or trimmed mean). Gene expression for individual cells is available for download at https://celltypes.brain-map.org/rnaseq/

Manage Gene List
Add genes of interest by clicking Add Gene in the white bar near the top right corner of the screen. Search for the gene’s symbol, e.g. “Chodl,” and it will appear in the top section of the heatmap.
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Alternatively, users can add multiple genes at a time. Click Add Gene in the white bar near the top right corner of the screen. Then click Add Multiple Genes and type or paste in a list gene symbols. The gene symbols can be delimited by any common delimiter.
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Move a genes up or down by hovering over the gene symbol and clicking the up or down arrow.
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Hide a gene by hovering over the gene symbol and clicking for more options.
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Select Cell Types
Click on a cell type or its column to highlight expression values for that cell type.
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Click on a higher level taxon to highlight expression values for all of its cell types.

If you select a cell type, you can toggle to the Scatterplot view to see that cell type’s distribution in tSNE/UMAP space.


Connect to Other Tools
Toggle over to the Scatterplot to see gene expression in tSNE or UMAP space. Hover over the gene symbol in the Heatmap view, and click the “Plot” option.
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For Mouse data, users can launch the Allen Mouse Brain Atlas to see a gene’s spatial distribution based on ISH data. Click the gene symbol in the heatmap view, and choose View in Mouse Brain Atlas.
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Customize Visualization
Toggle the color map by clicking on the current selection in the bottom of the screen.