Question: How to determine the surface markers in a gene list
1
gravatar for sadeghdavoudi
20 months ago by
sadeghdavoudi10 wrote:

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!

rna-seq gene • 1.5k views
ADD COMMENTlink modified 15 months ago by kristoffer.vittingseerup3.0k • written 20 months ago by sadeghdavoudi10
2

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

ADD REPLYlink written 20 months ago by bernatgel2.4k

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.

ADD REPLYlink written 15 months ago by tara.mcintyre0

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.

ADD REPLYlink written 15 months ago by rbronste340

Great question. Waiting for correct answers

ADD REPLYlink written 15 months ago by Shicheng Guo8.0k
1
gravatar for Jean-Karim Heriche
15 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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

ADD COMMENTlink written 15 months ago by Jean-Karim Heriche21k
1

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

ADD REPLYlink written 15 months ago by Shicheng Guo8.0k
0
gravatar for kristoffer.vittingseerup
15 months ago by
European Union
kristoffer.vittingseerup3.0k wrote:

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

ADD COMMENTlink written 15 months ago by kristoffer.vittingseerup3.0k
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