ZEBRA
How to use this database
Here, you can find an overview of the different views/analyses that the web server provides.
The general workflow for each analysis consists of the following steps:
- First, select what dataset to analyze. There are currently four different datasets, human and mouse, both with cortex and non-cortex samples. Precalculated cross-region DEG comparisons are also selectable (see Regional differential expression below). To select a dataset, click on the dropdown menu in the top left corner of the page and select the desired dataset.
- Next, select what analysis/view you want to perform. All available views in the left sidebar are further explained below (and via tooltip).
- In the next step adapt the parameters in the sidebar to your needs. Each parameter is explained with a tooltip (hover on the symbol). The page is automatically refreshed after a few seconds.
- Finally, you can download all plots by clicking on the camera symbol in the top left corner that appears when hovering over the plots. Tables can be downloaded via the Excel button. The data sets are also available for download in the Downloads section.
For more information on data curation and processing, as well as terminology, please refer to the information section.
The embedding view allows to color cells in a UMAP visualization by category. This includes discrete factors like Condition or Data set, as well as continuous factors like Age or Gene expression.
To visualize the expression of particular genes, first select Gene Expression in the Color UMAP by dropdown, then select a gene in the appearing Gene dropdown.
The plots support basic plotly navigation. Elements can be hidden by clicking on them in the legend. When hovering over a plot, a toolbar appears in its top left corner.
Analyze the data set composition in terms of cell type, condition, or other categories. The bar chart can be grouped into two categories at the same time or in the Group Bars By dropdown. Normalization toggles between showing counts and normalizing each group to one to show proportions. Additionally, you can choose between plotting bars side by side or stack bars per group.
The plots support basic plotly navigation. Elements can be hidden by clicking on them in the legend. When hovering over a plot, a toolbar appears in its top left corner.
Show a table of marker genes per cell type (differentially expressed genes). The marker genes are determined on control (healthy) samples. The web page only shows the top 200 genes per cell type. The table can be searched, re-ordered, and downloaded.
The complete DEG table can be downloaded in the download section.
Show the differential expression of your selected genes across conditions and data sets.
The top violin plot shows the mean normalized gene expression of the selected gene for different categories like the condition.
The bottom table shows the results of a DEG analysis for the selected gene, where each row corresponds to a comparison of the selected category (e.g., condition) against control samples.
The plots support basic plotly navigation. Elements can be hidden by clicking on them in the legend. When hovering over a plot, a toolbar appears in its top left corner.
Show the differential expression of each cell type (cluster) between cortex and non-cortex regions.
Select the combined datasets for human and mouse in the top left dataset dropdown. Then select the two cell types you want to compare in the respective dropdowns. The tables can be downloaded to Excel.
Show the mean expression of a selected gene, grouped by categories of your choice. Like the Data set composition page, two categories can be selected for a finer-grained comparison. For example, the mean normalized expression across different conditions can be compared for each age group.
The plots support basic plotly navigation. Elements can be hidden by clicking on them in the legend. When hovering over a plot, a toolbar appears in its top left corner.