In the HGNC database, there are "Previous symbols & names" and "Synonyms" fields which I would like to retrieve for my genes. I wanted to use biomaRt for that, but I don't know if HGNC mart exists biomart.org portal doesn't work since Thursday, so I can't even run listMarts()), or if I can get it via other marts like Ensembl.
What HGNC calls "previous symbols" are called "aliases" by the NCBI.
You can download the NCBI gene information file from
ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
When unzipped, this is a tab-delimited file with a column containing all aliases for each gene.
Alternatively the same information is packaged into the org.Hs.egALIAS2EG object of the org.Hs.eg.db package.
Alternatively you can convert previous to current symbols using limma's alias2Symbol() function, for example:
> library(limma)
> alias2Symbol("BIM")
[1] "BCL2L11"
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alias2Symbol is really a useful tool inside limma, but I don't know if it's outdated or what but I've detected some mistakes when retrieving approved symbols from alias (p.e. with genes FAM46C, MGEA5, MKL1, MKL2, LHFP, KIAA1524, where alias2Symbol doesn't transform them when the approved symbols are different). Is there an option to do it using biomaRt?
alias2Symbol is not outdated and does not make mistakes in conversion. It gives the correct result for all the genes you mention, for example
> alias2Symbol("FAM46C") [1] "TENT5C"It was me the one outdated sorry. I had the 3.32.2 version of the package and after updating to the actual version the problem was solved. My apologies