Getting Started with the Transcriptomics Explorer

Overview
The Transcriptomics Explorer enables researchers to visualize and analyze transcriptomics data and transcriptomic cell types for both mouse and human, all directly in a web browser. This product is an active area of development for the Allen Institute for Brain Science, and new features are released regularly. A previous version of this tool - called the RNA-seq Data Navigator - is still available for both mouse and human.

Currently researchers can:

  • Explore a gene expression heatmap across cell types in the dataset, and search for genes of interest to inspect
  • Explore a tSNE visualization of all cells in the dataset, colored by cell types or expression of genes of interest
  • Visualize a dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions
  • Find a cell type of interest in one visualization and see its characteristics in a different visualization
  • Download data files, including cell-level gene expression and taxonomic metadata and structure

In 2020, new functionality will enable researchers to:

  • Filter the dataset by cells’ sampling dimensions, quantified features, and annotations
  • Use correlation and differential searches to find similar genes and genes that differentiate cell types
  • Compare mouse and human cell types based on their gene expression

Toggling Visualizations
Toggle between the three visualizations by clicking on the “Visualizations” menu in the white bar near the top left corner of the screen.
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Toggling Datasets
Toggle between datasets by clicking on the menu in the black bar near the top left corner of the screen.
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Explore Gene Expression
The Heatmap visualization shows a heatmap of gene expression across the taxonomy of Cell Types for the 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/

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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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.

Examine Cell Types in tSNE space
The tSNE visualization shows each cell in the dataset in a 2D tSNE plot. By default, the dots (cells) are colored by their cell type assignment. At a glance, most cells in a single type are visually grouped together in tSNE space, but not all. Zoom in/out and pan to examine cell types of interest.

Click on a cell to highlight all cells of the same type.

Examine Gene Expression in tSNE space
To color the cells by expression of a gene, click the “Color By” menu near the top left of the screen.
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Choose a gene that you already have on the heatmap, or search for a gene using gene symbol.

Visualize a Dataset’s Sampling Strategy
The Sampling Strategy visualization illustrates the distribution of cells in the dataset across classes, subclasses, and dimensions of the experimental design, such as brain region. The area of each blue dot represents the proportion of cells with the corresponding sampling dimension (row) and cell type (column).

Click on a cell type or its column to highlight the representation of that cell type across the sampling dimensions. Click on a higher level taxon to representation of all its cell types.

Download a Dataset’s Files
Several files are available for download, including cell-level gene expression, taxonomic structure and labels, and cell annotations. Click “Download Data” in the bottom left part of the screen and choose the files of interest from the Download table.

Currently, the entire dataset must be downloaded as a whole. In 2020 it will be possible to download files for targeted subsets of the dataset.

Cell Type Nomenclature & Taxonomy
The Cell Types nomenclature is described here: https://portal.brain-map.org/explore/classes/nomenclature

The organization of the Cell Types is structured in a species-specific taxonomy. Taxonomies and their metadata are downloadable here: http://celltypes.brain-map.org/rnaseq.