Hello,
I have a long list of transcription factor protein names and IDs for chicken. I want to get the corresponding gene names and gene IDs. How can I do that in a quick way as it is tedious to look for each protein separately. Can it be done in R?
The file looks like this:
Ensembl Protein ID Description
ENSGALP00000000063 cold shock domain containing C2, RNA binding [Source:HGNC Symbol;Acc:30359]
ENSGALP00000000227 myogenin (myogenic factor 4) [Source:RefSeq peptide;Acc:NP_989515]
ENSGALP00000000232 Kruppel-like factor 3 (basic) [Source:HGNC Symbol;Acc:16516]
ENSGALP00000000311 Sp2 transcription factor [Source:HGNC Symbol;Acc:11207]
ENSGALP00000000406 Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:E1C668]
Similarly I have Affymetrix gene IDs for chicken that I want to map to gene names and it looks like this:
Gga.4558.2.S1_s_at
GgaAffx.21351.1.S1_s_at
Gga.11474.1.S1_a_at
GgaAffx.21384.1.S1_s_at
Gga.17952.1.S1_at
Gga.7798.1.S1_at
Gga.11798.1.S1_s_at
GgaAffx.12750.1.S1_s_at
GgaAffx.7263.1.S1_at
Gga.9266.1.S1_a_at
Gga.752.1.S1_at
Gga.16740.1.S1_at
GgaAffx.10527.1.S1_at
Gga.19004.1.S1_at
How can I map these to genes names in R? Many thanks.
1 answer
You haven't said which type of protein IDs you have but I'll assume they're refseq / ensembl / entrez or similar common IDs.
It can be done in R, for example using the biomaRt bioconductor package, alternatively you could strip your list of IDs and use them as a filter in ensembl biomart directly, you can then select which identifiers you require as results.
Similarly, biomart central has an ID conversion tool which will go from protein -> gene ID.
Edit: Now you've added your IDs as examples, the most straightforward method of conversion (depending on how many you have) is to use biomart's gene ID conversion tool
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Transform Affymetrix Ids Between Species
written by mimA •
Can you show us, how the data looks like, just the
head.And edit what you posted; it needs spaces.