How can I obtain the marker gene list of Mouse snRNAseq in class level

Technical
1

Thanks for developing Cell Type Mapper, it is very useful to annotate our data with Allen taxonomy. But I encountered some problem when I annotated my own snRNAseq data:
I would like to draw a bubble plot to show the marker gene of different classes, but according the annotation
The MapMyCells website provides a .xlsm file, which seems to contain the desired information: cl.df_CCN202307220.xlsx

I can not find the gene marker in class level. There are only marker genes in cluster level (colname: cluster.markers.combo), but it is too detailed for me. So how can I obtain the marker gene list of Mouse snRNAseq in class level?

Thank you for your assistance.

2

Hi, YSviann

We didn’t provide class marker genes because they are very difficult to identify. Very few classes have markers that span the whole class yet still specific. We might provide such list in the next version after relaxing the marker selection criteria substantially.

3

For what it’s worth:

If you want to see the marker genes that MapMyCells uses, they can be found in the JSON file referenced on this page. This won’t give you marker genes unique to each class, but there is a set of a few hundred marker genes used to distinguish between classes listed under 'None' in the dict represented by that JSON file. Maybe that will help.

Note that MapMyCells uses a quirky notion of marker genes. The marker genes listed under class/classA are actually the marker genes used to distinguish between all of the child nodes of class/classA in the taxonomy. Since “class” is the highest level of the taxonomy, the markers listed under 'None' are the markers used to distinguish between the classes (i.e. the children of the root node of the taxonomy). This is documented on this page.

4

Thanks! It do helps me a lot!

5

Thank you very much. It do helps me a lot!