Hello,
Thank you for the fantastic tool!
I’ve been searching for the list of gene markers used for annotating human region-specific subtypes in MapMyCells. I was able to find the mouse annotation table here: Whole adult mouse brain taxonomy of cell types — Allen Brain Cell Atlas - Data Access, but I haven’t been able to locate the corresponding information for human data.
Could you please point me to the relevant resource if it’s available?
Thanks again!
Hello,
I’m actually not sure that the markers you found for Whole Mouse Brain are the markers used by MapMyCells.
MapMyCells defines marker genes a little differently than they are generallly defined. Rather than saying “the marker genes for CellTypeA are the genes whose expression uniquely distinguishes CellTypeA”, MapMyCells uses a table of marker genes defined such that “the marker genes for CellTypeA are the genes that can best be used to discriminate between all the children of CellTypeA.” Those marker genes are recorded in a file whose schema is defined here.
To get the actual marker gene tables (as defined above) used by MapMyCells, consult this page, which includes links to where all of the data files backing the on-line MapMyCells taxonomies, including Whole Human Brain and SEA-AD, may be found.
Please let me know if anything is unclear.
Hello,
Apologies for the delayed response, and thank you so much for your help!
I’m currently working with bulk RNA-seq data from various brain regions, and my goal is to identify marker genes specific to certain areas such as the amygdala, temporal neocortex, or middle temporal gyrus. I’d like to explore the expression of these genes in my dataset to assess regional specificity.
I’m having a bit of trouble finding the actual marker gene tables, would you happen to have a link to a resource that includes this information for the Whole Human Brain?
Thanks again!
The Whole Human Brain data assets (marker gene lookup table and average gene expression by cell type file) are available here.
(Sorry; I can see how the links in that GitHub documentation page might be a little confusing)