This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convert Gene stable ID to Gene Symbol

Hello

I need to convert gene stable ID like this (ENSMUSG00000028461.12) to gene name. I used Biomart and I have a list of gene stable ID. I don't know how to join mine list with Biomart together, because Biomart gene stable ID list has not the decimal number in ID, do you have any idea?

thanks

gene rna-seq next-gen
• 4,306 views • link
updated by finswimmer finswimmer • written by lkianmehr lkianmehr

2 answers

Hello,

I don't understand whether your problem is that your input has version numbers or that the output of biomart hasn't. Nevertheless we can solve both:

For the input choose under Filters the category Input external references ID list and select in the drop down Gene stable ID(s) with version.

For the output choose under Attributes Gene stable ID version in the category GENE.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

I think the numbers after the decimal (.12 in your example) is the version of that particular gene. Eg: http://asia.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000028461;r=4:43492900-43495921

So drop the numbers after the decimal (and the decimal too).

• 1 views • link
written by Mark Mark

Log in to answer this question.

More posts like this