MapMyCells marker genes of classes

Cell Taxonomies
1

Thanks for developing MapMyCells, it is very useful to annotate our data with Allen taxonomy.

We got class/subclass predictions from mapmycells, and now we’re trying to validate those with marker gene expression.

Currently, I am seeking information on marker genes that define each class and subclass in comparison to all others.

The MapMyCells website provides a .xlsm file, which seems to contain the desired information: cl.df_CCN202307220.xlsx.

Questions I have:

  1. Can I accurately state that the columns “subclass.markers.combo” and “subclass.tf.markers.combo” contain the genes and transcription factors, respectively, that distinguish each subclass from all others?
  2. I am struggling to locate the equivalent information (i.e., the set of marker genes) for the class level annotation. Is there a specific file or location where I can obtain this type of information?

Thank you for your assistance.

2

Hi @mbatiuk ,

Thank you for your interest in MapMyCells. In response to your first question, yes, the genes listed in those columns distinguish one subclass from all other subclasses. For your second question, we have not generated a class marker list. Please let me know if you have any additional questions.

Best,
Elysha Fiabane
Product Manager, MapMyCells

3

Hi Elysha,

Thank you for your response.

It is crucial for us to have class level marker genes for mouse brain.

We use MapMyCells to annotate cell types in our dataset

But we as well use it to identify contaminant cell types that derive from nearby brain regions - and being taken during dissection of the region of interest

Thus before we exclude any class of cells from analysis derived from elsewhere than region of interest we really need to verify and make sure by using marker genes that those classes of cells are indeed from thalamus and not from hippocampus

Do you know any way to get class level marker genes?

I believe MapMyCells uses class level markers to divide cells into classes on the first hierarchical split - so this list of genes should be available somewhere

Thank you in advance for any help,
Mykhailo