Question: Find Gene Symbol/Gene Name According To Orf Accession
4
gravatar for Bioscientist
3.6 years ago by
Bioscientist1.4k
Bioscientist1.4k wrote:

I have a list of ORF accession like NM_000163; I want to know their corresponding gene name I tried on UCSC genome table but cannot figure out

thx

gene • 806 views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 0 • written 3.6 years ago by Bioscientist1.4k
5
gravatar for Pierre Lindenbaum
3.6 years ago by
France
Pierre Lindenbaum74k wrote:

I can find your acc in the refGene table

$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select name,name2,chrom,txStart,txEnd from refGene where name="NM_000163"\G'
*************************** 1. row ***************************
   name: NM_000163
  name2: GHR
  chrom: chr5
txStart: 42423876
  txEnd: 42721980
ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum74k
2
gravatar for Woa
3.6 years ago by
Woa2.4k
United States
Woa2.4k wrote:

Download the sequences and parse the files to get the gene names.

http://biostar.stackexchange.com/questions/13396/fetch-many-files-with-accession-number-output-file-format-is-coding-sequences-in/13402#13402

This piece of code will fetch the gene name:

my @tags=qw/gene/;
my ($feat_object)=@cds_features;
my ($gene_name)=map{$feat_object->get_tag_values($_);}@tags;
ADD COMMENTlink written 3.6 years ago by Woa2.4k
2
gravatar for Bert Overduin
3.6 years ago by
Bert Overduin3.4k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.4k wrote:

You can use Ensembl BioMart for this:

Step 1:

  • Go to the Ensembl homepage.
  • Click on the ‘BioMart’ link on the toolbar.
  • Choose the ‘Ensembl Genes 65’ database.
  • Choose the ‘Homo sapiens genes (GRCh37.p5)’ dataset.

Step 2:

  • Click on ‘Filters’ in the left panel.
  • Expand the ‘GENE’ section by clicking on the + box.
  • Select ‘ID list limit – RefSeq mRNA ID(s)’.
  • Enter the list of RefSeq IDs for your genes in the text box (either comma separated or as a list).

Step 3:

  • Click on ‘Attributes’ in the left panel.
  • Select the ‘Features’ attributes page.
  • Expand the ‘GENE’ section by clicking on the + box.
  • Deselect ‘Ensembl Gene ID' and 'Ensembl Transcript ID’.
  • Expand the ‘EXTERNAL’ section by clicking on the + box.
  • Select ‘RefSeq mRNA’ and ‘HGNC symbol’.

Step 4:

  • Click the [Results] button on the toolbar.
  • Select ‘View All rows as HTML’ or export all results to a file. Tick the box ‘Unique results only’.

For your example this gives me:

RefSeq mRNA HGNC symbol

NM_000163 GHR

Hope this helps.

ADD COMMENTlink written 3.6 years ago by Bert Overduin3.4k
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