Corals cell atlas

Cell atlases

This section allows the exploration of the datasets in a species-focused manner and from different perspectives.

First, select your dataset of interest and click on Generate cell atlas.

Then you can explore four pages:

Overview – metacells and single-cells 2D projection, cell type labels, and metacell heatmap showing expression of highly variable genes. Here you can download the metacell regularized gene expression matrix and the raw single-cell UMI counts matrix.

Single gene query – select your gene of interest by geneID or launch a BLAST search with your protein of interest (you need to select the hit of interest, if any).

Multiple genes query – this allows the visualization of multiple genes at once. You can search genes by name or by Pfam domain (e.g. “Myosin_head/” will retrieve you all the genes with a myosin domain) and you can also upload a list of interest. We also provide predefined lists of genes for different families/sets of function (e.g. cell adhesion, GPCRs, transcription factors),

Cell type markers – first you need to select one or more metacells or a cell type of interest. Then, you need to select an expression threshold for marker selection. Optionally, you can request that the gene is expressed in all other metacells below a certain threshold (in each of them – absolute – or as a median value).
This generates a table of the top marker genes fulfilling the selected criteria. You can sort them using different metrics and also specifically select transcription factors. This table can be downloaded.