Single-cell cluster : up- vs down-regulated marker genes

Question

[PR]

Hello All,

I would like to know what the experts feel about defining single-cell clusters using up-regulated versus down-regulated marker genes. There is this general view that down-regulated marker genes are ambiguous (and justifiably so), and hence clusters are much better defined by considering only the up-regulated marker genes compared to the rest of the cells in the data. While I understand the overall reasoning behind this, packages do offer the option of obtaining down-regulated marker genes as well. So, what are the caveats of including down-regulated genes in the list? If any, what are the advantages?

Would really appreciate any replies!

Thanks.

Answer 1

[igor]

Clusters are generally defined by all the genes (or variable genes to be more precise). However, people usually only look at the up-regulated genes because those are easier to interpret. A gene present in only one cluster can serve as a good marker. Cell types are generally described by their markers. For example, CD79a is a B-cell marker. If you see it expressed in a population, you are likely looking at B-cells. However, if you don't see it, it's not particularly helpful.

[PR]

Thanks a lot for your response, Igor. That helps!