How To Convert Hgnc Gene Symbols To Gene Full Description?

Question

[sarahmanderni]

Hi,

I have a list of gene symbols (HGNC) and need to get the full description of them.Like having gene "saa1" (human) I need to get "Serum Amyloid A1". I know DAVID conversion tool but I could not find which option to choose for getting the gene full description. Thanks

Answer 1

[Neilfws]

There are a few solutions to this problem. There might be a file for download from the HGNC website which contains symbols and names.

Another solution is the HGNC REST service. From the command line, for example:

curl http://rest.genenames.org/fetch/symbol/SAA1 > saa1.xml

You would then need to parse the XML (or JSON) file to extract the name (using grep here, just to show the relevant line):

grep "str name=\"name\"" saa1.xml
# <str name="name">serum amyloid A1</str>

HGNC also have a BioMart server, which is an excellent option. Use Approved Symbol for the filter and Approved Symbol + Approved Name for the attributes. Using SAA1 as the filter value you should see this result. There is also programmatic access to BioMart (e.g. R biomaRt).

[sarahmanderni]

Thanks for the answer. Just I couldnt find if it is possible to send list of gene symbols to HGNC BioMart server or not. As I an see it only accepts one gene symbol at any search, is that true? Moreover, biomaRT in R, can retrieve: hgnc ID, hgnc symbol and hgnc transcript IDs but not hgnc names. Or at list I could not find this attributes in the manual.

[Neilfws]

It is not very clear from the web interface, but you can separate multiple gene symbols using commas.

Not sure which biomaRt manual you are reading, but it will retrieve any attribute associated with the mart instance, just like the web interface.

You could also use the Ensembl BioMart server for this query, using HGNC Symbol as the filter and HGNC Symbol + Description as the attributes. Here is the result for SAA1. This interface has more options, but allows input of symbols one per line or upload of a file with symbols.