Hi all, I found it is pretty hard for me to construct a table which can match gene name and its corresponding protein name.
Say, I have a protein-encoding gene CD79A, and its protein should have the same name. However, for some genes, their proteins have different names, thus it is pretty hard for me to do the matching work. I have tried ensembl, but it only returend me with protein id rather than name.
I wonder if there are any databases or tools that I can use to access every pair of protein-gene with their name rathar than id or ensembl name. Thanks.
3 answers
Since that seems to be a human gene you give for example, I gather you mean for human genes though it is unstated in the post? There's a lot of resources.
I recall Zhenyu Zhang covered some here in a reply to another question with some experience informed comments included.
A mention of some possibilities I don't see there:
- The human equivalent for what I like for handling a lot of the aliases in yeast would be HumanMine. I see it has a Gene to Proteins template and a Protein to Gene template. You can adapt those and make custom queries. I don't know how extensive they are for handling all the aliases though.
- biomaRt is commonly used for this is my understanding.
- CD79A on GeneCards. That database may be helpful for checking the results of your table making effort.
You could try using EntrezDirect. An example below.
$ esearch -db gene -query "CD79A AND Pongo abelii [ORGN]" | efetch -format tabular
tax_id Org_name GeneID CurrentID Status Symbol Aliases description other_designations map_location chromosome genomic_nucleotide_accession.version start_position_on_the_genomic_accession end_position_on_the_genomic_accession orientation exon_count OMIM
9601 Pongo abelii 100460212 0 live IGBP1C IGBP1 family member C immunoglobulin-binding protein 1 family member C|immunoglobulin (CD79A) binding protein 1 family member C|immunoglobulin-binding protein 1 pseudogene 17 NC_072002.1 59478723 59510416 plus 2
9601 Pongo abelii 100445445 0 live IGBP1 CR201_G0029124 immunoglobulin binding protein 1 immunoglobulin-binding protein 1|immunoglobulin (CD79A) binding protein 1 X NC_072008.1 74965522 74998999 plus 8
9601 Pongo abelii 100438225 0 live CD79A CR201_G0044077 CD79a molecule B-cell antigen receptor complex-associated protein alpha chain 19 NC_072004.1 54143628 54147820 plus 5
You can submit your list of gene names, together with an organism name / taxonomy identifier to the UniProt IDmapping service at https://www.uniprot.org/id-mapping Select to map from (UniProt>)Gene Name to UniProtKB.
Your result table can be customized to include only the columns you are finding of interest in this context. Please don't hesitate to contact the UniProt helpdesk if you have any additional questions.
And for those interested in using that great resource programmatically, I have some resources and links to examples using the excellent Unipressed, see the bottom of my post here.
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