How to determine the surface markers in a gene list

Question

[sadeghdavoudi]

Hi,

I have a gene list ~400 genes expressed in a cell type, and I want to determine which ones, upon translation, are presented on the cell surface that I can potentially use for FACS (fluorecencse activated cell sorting) . Does anyone have any suggestions other than googling them one by one? Is there a database of cell surface proteins that I can run this against.

Thanks!

[bernatgel]

I would probably annotate them with Gene Ontology, with the "Cellular Compartment" part, and then look for membrane associated terms.

[tara.mcintyre]

Hi @sadeghdavoudi, did you have any luck with this? I am trying to do the same. Unfortuantely, when I annotate using GO and "cellular components" nothing in the plasma membrane comes up.

[rbronste]

I would think that parsing by the domain families present on the proteins these genes encode would be a useful approach. Another potential route is to look at which of the proteins these genes encode are routinely myristoylated as that would pretty much guarantee membrane targeting.

[Shicheng Guo]

Great question. Waiting for correct answers

Answer 1

[Jean-Karim Heriche]

In addition to previous suggestions of looking for relevant protein domains and GO annotations, you could also check which of the proteins in your list are known or putative cell surface proteins in the following databases:
- cell surface protein atlas
- extracellular matrix interaction database
- Human Protein Atlas

[Shicheng Guo]

Nice. Maybe we can thinking about to based a algorithm to weight them and give a prediction

Answer 2

[Kristoffer Vitting-Seerup]

I would suggest to use data from the CellPhoneAtlas - the database that accompanied this recent Nature paper.