Some HGNC Gene Symbols have synonyms that are more familiar to biologists of particular breeds. For example, "SELL" means little to a immunologist, whereas SELL's alias "CD62L", means rather a lot. Showing the biologist a list of gene names and saying "do any of these ring bells" seems to be an important part of the process of selecting important genes (or, rather, its validation), and hence I'd like to make sure they see the gene names that make sense to them.
My question, therefore, is: does anyone know a simple method to retrieve gene synonyms? I don't want to do any enrichment, or clustering or normalisation, I just need a mapping from HGNC symbol -> synonyms. I can't quite figure out how to persuade biomart to do this.
In addition, are there certain sets of symbols that are preferred by some communities? For example, do I need to search through all the synonymous symbols, or can I just ask biomart (or something) to return a particular set of gene symbols?
Four years since you've posted this, I've just found it. Exactly what I was looking for, thanks. Similarly to the initial poster, I am just interested in H. sapiens genes. This means you don't need to download the rather large full list from Entrez but can limit yourself to:
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
Very useful, thanks!
One precision. If you are searching for official symbol (=
$11
), sets the-F
option to "\t". For example:I have an R wrapper for this at https://github.com/oganm/geneSynonym. It extracts synonym information about the species of interest and allows you to query any gene symbol for synonyms.