How To Convert Refseq Id To Gene Symbol As Pitx1

Question

[Hamilton]

Hi, how can i convert refseqids (mouse) to gene symbols?

Answer 1

[Pierre Lindenbaum]

you could use the UCSC database for mus musculus:

$ mysql   --user=genome --host=genome-mysql.cse.ucsc.edu -A   -D mm9  \
  -e "select distinct refseq,geneSymbol from kgXref where refseq in ('NM_008866','NM_011541','NM_011011') "
+-----------+------------+
| refseq    | geneSymbol |
+-----------+------------+
| NM_008866 | Lypla1     |
| NM_011011 | Oprk1      |
| NM_011541 | Tcea1      |
+-----------+------------+

Answer 2

[Newgene]

use MyGene.info API, python and R clients are available.

For Python:

pip install mygene

then

import mygene
mg = mygene.MyGeneInfo()
mg.querymany(['NM_008866','NM_011541','NM_011011'], scopes='refseq')

that's it!

Answer 3

[Curiosity]

You could download refseq gene list in "all" format instead of "BED" format using Galaxy http://main.g2.bx.psu.edu/ and then print the selected columns using unix command.

Use the following command

 awk '{print $2"\t"$13}' all_refseq.list

Ex: NM_001195025 Nuak2