In the header of page, users can perform a comprehensive search based on ID.
A drop-down menu on the left helps users narrow down their queries. The optional categories are species, tissue, cell type, gene, project, dataset.
The examples of detail page are shown below.
In the search page, users can perform a advanced search for gene, cell type, project, or dataset.
Users can perform a conditional search to narrow down the target.
The examples of detail page are shown above.
Cell type identification
In the cell type identification page, users can input multiple genes and set filtering parameters to obtain the marker information of these genes.
Users can select interested marker information for visualization.
This is a result case.
In the exression page, users can click nodes in the folded tree to obtain information about datasets of cell types.
The users choose one or more cell clusters, which can come from the same or multiple cell types, and then queries through symbol or manually insets gene ID. After running, visualization of expression profile will be carried out. The returned result is usually a dynamic interactive heat map.
When the specified cell cluster or gene ID is one, a bar graph will be generated.
If there is marker relationship among the genes and cell types selected by users, a marker relationship figure of these genes and cell types will also be generated.
Users can paste sequences or upload files to query FishSCT based on sequence similarity.
General search options provide a parameter named db, which allows users to perform similarity searches for one or all species in FishSCT.
Other parameters are set by default for users, and the output format is tabular with comment lines, which is our most recommended.
In the download page, FishSCT provides marker information downloads for each species and expression profile downloads for each dataset.
The information of download marker files include gene id, symbol, location, marker class, tissue, cell type, p value, and evidence.