How to Find Cell Type From Marker Genes (SC-RNA-Seq)

Question

[gtasource]

Hey guys,

I know that for a lot of people, looking at the market genes of a cluster is something that is done manually. Obviously, if you know a lot about the tissue you are dealing with, it’ll be easier to say that these marker genes are indicative of this cell type. But what if you have no idea? Do you refer to a database, literature? How else could you decide the clusters face in this situation?

Thanks!

Answer 1

[Kevin Blighe]

Apologies that nobody answered. Most researchers do indeed just use pre-compiled gene lists in order to infer cell-types in their data. Sometimes, employing an algorithm to do the work may not even be required, as certain cell-types are quite obvious, for example, scRNA-seq clusters that highly express CD56 are going to be on the natural killer cell lineage.

I believe a colleague recently searched for some programs that can infer cell-types 'de novo' without any pre-compiled lists; however, these are still going to be utilising some gene-to-celltype mapping in the background (and I cannot recall the name of the program).

As larger tissue-profiling studies are published and data is made available, I suspect that we will be able to, one day, predict most cell / tissue-types with high accuracy.

One of the earlier tissue-specific studies was actually from the FANTOM consortium, out of Rijken in Japan, and it was on this data that we constructed our own cell-type prediction algorithm for this work: Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes (I no longer work there).

Kevin