Question: Convert Refseq Id To Gene Name
2
gravatar for hicsuntdrac0nis
4.5 years ago by
hicsuntdrac0nis190 wrote:

I'm trying to convert a list of RefSeq IDs to the Gene Symbol . . . I can do it for Ensembl using http://genome.ucsc.edu/cgi-bin/hgTables [Track -> Ensembl Genes : Table -> ensemblToGeneName]

I can import a list like:

ENSMUST00000000219
ENSMUST00000000450
ENSMUST00000001156
ENSMUST00000001319
ENSMUST00000001559

and get a table that looks like this:

ENSMUST00000000219    Th
ENSMUST00000000450    Pparg
ENSMUST00000001156    Cfp
ENSMUST00000001319    Efnb2
ENSMUST00000001559    Itfg2

and life is super easy . . . I can't figure out how to do something similar with RefSeq IDs!

I tried using http://idconverter.bioinfo.cnio.es/IDconverter.php which worked the best out of all the converters suggested by http://www.shodhaka.com/cgi-bin/startbioinfo/simpleresources.pl?tn=Gene%20ID%20conversion&sort=Rank%20by%20usage%20frequency but it wasn't recognizing some of the transcripts and its really annoying

Does anyone know how to import a list of RefSeq genes:

NM_001081045 NM_027801 NM_001267620 NM_028121 NM_001167748

and get out the Gene Symbols:

Kansl1 2610015P09Rik Ankzf1 Adpgk Egfem1

gene refseq convert • 26k views
ADD COMMENTlink modified 2.5 years ago by tangming20052.2k • written 4.5 years ago by hicsuntdrac0nis190
1

Please search this site for the many similar questions and answers, which explain how to use BioMart.

ADD REPLYlink written 4.5 years ago by Neilfws47k

Gene ID conversion tool

ADD REPLYlink written 4.5 years ago by Michael Dondrup43k
4
gravatar for Ashutosh Pandey
4.5 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Try:

$ mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e "select name,name2 from refGene" > Refseq2Gene.txt

This will give u the mapping file. For mouse replace hg19 with mm10.

ADD COMMENTlink modified 4.5 years ago by Alex Reynolds21k • written 4.5 years ago by Ashutosh Pandey11k

Copy and paste in excel and do VLOOKUP for your genes.

ADD REPLYlink written 4.5 years ago by Ashutosh Pandey11k
8

10 out of 10 scientists agree: don't use Excel!

ADD REPLYlink written 4.5 years ago by Steve Lianoglou4.8k
1

Huh!! Its funny that they even have a paper about it.

ADD REPLYlink written 4.5 years ago by Ashutosh Pandey11k

Do biologists not classify as scientists then?

ADD REPLYlink written 4.5 years ago by Michael Dondrup43k
3

Of course we do, which is why we don't use Excel :).

ADD REPLYlink written 4.5 years ago by terdon400

You know the old adage ... if it doesn't have the word "science" in the title, then it's not a real science.

Computer Science all the way, baby ... wooo hoooo!

Oh ... no, wait ...

ADD REPLYlink written 4.5 years ago by Steve Lianoglou4.8k

i'm sorry but I get really confused when trying to use Open Source databases through Terminal on my Mac. can you direct me towards somewhere where I can learn ?

ADD REPLYlink written 4.5 years ago by hicsuntdrac0nis190

Hi Ashutosh, I don't know if you can get my message but I have a question for you. Your code for retrieving mapping file from human refGene database only gives locus and gene symbol. How do I get gi number and reseq protein number from it? Thank you.

ADD REPLYlink written 2.5 years ago by grayapply2009150

How can I do that for UCSC Genes instead of refseq Genes?

Thank you

ADD REPLYlink modified 16 months ago • written 16 months ago by silas00840
3
gravatar for vaskin90
4.5 years ago by
vaskin90260
Milan, Italy
vaskin90260 wrote:

You could try bioDBnet converter: http://biodbnet.abcc.ncifcrf.gov/db/db2db.php

ADD COMMENTlink written 4.5 years ago by vaskin90260
2
gravatar for Ashutosh Pandey
4.5 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

An alternate way would be to go to

1) http://genome.ucsc.edu/cgi-bin/hgTables?command=start

2) Select your genome and assembly and selct Genes and Gene Prediction track as group.

3) Select Refseq Genes as track

4) Select refGene as a table and then output the file.

Then you can use a script or excel to map your refseqids to gene names. Make sure you follow what Steve mentioned in the comment section. Also, have u ever used DAVID (http://david.abcc.ncifcrf.gov/conversion.jsp)

ADD COMMENTlink written 4.5 years ago by Ashutosh Pandey11k

Upvote for this answer. Using the table browser is better than the biomart if you have a huge number of IDs to be converted.

ADD REPLYlink written 9 months ago by anniepyim0
2
gravatar for tangming2005
2.5 years ago by
tangming20052.2k
Houston/MD Anderson Cancer Center
tangming20052.2k wrote:

You can use Biomart http://crazyhottommy.blogspot.com/2014/09/converting-gene-ids-using-bioconductor.html

ADD COMMENTlink written 2.5 years ago by tangming20052.2k
1
gravatar for plaschkej
4.5 years ago by
plaschkej10
plaschkej10 wrote:

Here is a bioperl script

#!/bin/perl
use warnings;
use strict;
use Bio::Perl;
$| = 1;

my $db = new Bio::DB::RefSeq;

print "Input RefSeq ID: ";
my $refseq = <STDIN>;
chomp($refseq);

my $seq = get_sequence('refseq',$refseq);

# most of the time RefSeq_ID eq RefSeq acc
#my $seq = $db->get_Seq_by_id($refseq); # RefSeq ID
#print "accession is ", $seq->accession_number, "\n";

if ($seq->desc =~ /\((\w+)\)/) {
    print"found: $1\n";
    print $seq->desc;
}
else
{
    print "defintion is ", $seq->desc, "\n";
}
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by plaschkej10

Hi, I am not perl person - would be possible to change this script to paste LIST of NM_numbers instead of typing to STDIN in cmd??

ADD REPLYlink written 8 months ago by Paul930
0
gravatar for tangming2005
4.5 years ago by
tangming20052.2k
Houston/MD Anderson Cancer Center
tangming20052.2k wrote:

Cistrome/Galaxy can do it very easily. http://cistrome.org/ap/ In the tool box on the left:

Liftover/Others Convert between RefSeq, Gene Symbols to Entrez IDs using Bioconductor. Liftover Wig Files Liftover wig files [Galaxy]Convert genome coordinates between assemblies and genomes Standardize wig file Standardize a wig file to a given span Extract data from Wiggle Extract data for certain chromosome from a wiggle file Extract data from Bed Extract data for certain chromosome from a BED file

ADD COMMENTlink written 4.5 years ago by tangming20052.2k
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