tool to convert cytokine name for pathway enrichment?

Question

[boaty]

Hi guy,

I found it is super difficult to convert cytokine names to suitable id for pathway enrichment. The mapability of my 200 cytokines was ~ 20%.

Is there any tools, website or a .txt file that marks cytokine name with its gene/protein name?

Thanks in advance.

test2 <- mapIds(x= org.Mm.eg.db,
            keys = cytoname,
            keytype = "SYMBOL",
            column = "ENTREZID")
test2

AR          Axl        CD27L         CD30         CD40       CXCL16     
NA        "26362"      NA             NA           NA           NA         
E-selectin  Fractalkine         GITR          HGF      IGFBP-2     
NA             NA                NA            NA          NA               
IGFBP-6        IGF-1     IL-12p70       IL-17E       IL-17F      
NA              NA           NA           NA           NA

[Jean-Karim Heriche]

How were your cytokines identified before you got to the name? If they were somehow identified by sequence, I'd go back and map the sequences to the reference genome you're using. If you got them as a list from some resource, go back to this resource and try to get gene IDs instead of names. Finally, you're trying to convert gene symbols but your list doesn't contain many of them (only one in the example you gave). Note that official mouse gene symbols don't contain hyphens and only the first letter is capitalized, e.g. the symbol for IGF-1 is Igf1.

[boaty]

Thank you.

you remind me, to call the platform and get the perfect names table. Thanks a lot for the explaining of mouse gene name, that's very useful.