Converting NCBI Entrez ID to Glyma ID

Question

[Bioinf_Questions]

Hi everyone. I used NCBI database for soybean genome data for RNASeq data analysis (differential expression). My results table generated by Deseq gave me the gene IDs (Entrez IDs), but I need the Glyma IDs and I Can't find anywhere a tools or site to convert Entrez Id in Glyma ID. Not even a list of correspondence. On a second note, does anyone know of a site/tool where a just need a list of genes (Entrez IDs) to get a functional annotation? I found one, but it requires Glyma ID. I have around 2000 genes I need o annotate. Doing it by hand would be very time consuming.

Thank you in advance for any help.

Answer 1

[GenoMax]

Here is what NCBI says about LOC gene ID:

Symbols beginning with LOC. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345.

You could try your luck with Entrezdirect, if following is sufficient

$ esearch -db gene -query LOC100101844 | esummary | xtract -pattern DocumentSummary -element Name,Description
LOC100101844    PR10-like protein

[Bioinf_Questions]

Ok. Thank you.