protein ID convert to gene name ID

Question

[dew]

Dear guys,

May I know if there is an R package for easily converting the protein ID to gene name?

Thanks a lot!

Best,

[Fadwa]

I think it's easy by bash You can use

Grep -o -f {protein ID} {Gene ID}

[ATpoint]

That's hardly an answer, it's neither in R as requested, nor do you say where to get the conversion tables from that are required.

[ATpoint]

That depends a bit on the type of IDs you have, but the answer is most like biomaRt, can you post an example?

[dew]

Thanks a lot! Left side is the protein ID, right side is the gene name by the online UniProt mapping tool. While the it shows more gene names were mapped than the protein ID numbers, so guess some protein ID also have multi mappings....

A0A075B6K4  IGLV3-10
A0A075B6S5  IGKV1-27
A0A0A0MRZ8  IGKV3D-11
A0A0B4J1V0  IGHV3-15
A0A0B4J1X5  IGHV3-74
A0A0C4DH42  IGHV3-66
A0A0C4DH69  IGKV1-9
A0A0C4DH73  IGKV1-12
A0A0J9YXX1  IGHV5-10-1

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db protein -query A0A075B6K4 | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name
IGLV3-10

For more than one ID (one per line in file test):

   $ for i in `cat test`; do printf ${i}"\t"; esearch -db protein -query ${i} | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name; done
    A0A075B6K4      IGLV3-10
    A0A075B6S5      IGKV1-27
    A0A0A0MRZ8      IGKV3D-11
    A0A0B4J1V0      IGHV3-15
    A0A0B4J1X5      IGHV3-74
    A0A0C4DH42      IGHV3-66
    A0A0C4DH69      IGKV1-9
    A0A0C4DH73      IGKV1-12
    A0A0J9YXX1      IGHV5-10-1

[dew]

Amazing! Thanks a lot! :) Best regards!