How can I identify membrane molecules within a gene list?

Question

[adri.vife]

Hello everybody,

I was wondering how can I identify if there are membrane molecules / receptors in a large list of genes. I tried with biomaRt in R to get the subcellular location but I did not success.

For example, given a list of genes like: COL6A3, ZEB2, PDGFRA, PCDH18 How can I check its subcellular location or even better, to find which one is a membrane molecule?

Thank you in advance,

[bernatgel]

You could annotate them with Gene Ontology terms (Cellular Compartment ontology) and check if there are any of the terms related to membrane. Not ideal, but should work.

[caggtaagtat]

You could use the filter in Biomart called "Limit to genes..." within the "PROTEIN DOMAINS AND FAMILIES" filter section. There is an option called "With transmembran helices". This setting should give you information about genes, which have at least one transcript that holds a transmembran helix. Though, I don't know if this information is validated or predicted, probably the latter.