mapping gene synonyms to uniprot recommended gene name

Question

[juncheng]

Hi,

I'm comparing the expression data of microarray and RNA-seq, but I got a problem about the gene names. A lot of the gene names used in microarray are synonyms, for example AOF2, which in RNA-seq is KDM1A. The gene names in RNA-seq are mostly uniprot recommended names. Is there any way to map the synonyms to the "default" gene names?

The ID mapping in uniprot seams gives me a long list of ID mapping result.

[cdsouthan]

This is a perennial issues but the supplier of the microarrays should have resolved the mappings for you. If the data sets are human the HGNC gene names (should be) the default but technically these are not protein names.

Answer 1

[Richard Smith]

You could try uploading the list to metabolicMine which contains human gene data. This will search synonyms and should find the official HGNC/NCBI gene symbols. For each entry that matches a synonym rather than an official symbol it will show you what it has matched before you add it to the saved list.

When you've created the list you can download the official gene symbols and see how many were resolved.

[juncheng]

thanks! Also I solve the problem already, hope can help others.