Question: convert pseudogene IDs in Gencode releases to HGNC gene symbols
0
gravatar for biocyberman
3.8 years ago by
biocyberman760
Denmark
biocyberman760 wrote:

The pseudogene file I downloaded from GeneCode looks like this:

 

chr10   Yale_UCSC       transcript      5304431 5304865 .       -       .       gene_id "PGOHUM00000289731"; transcript_id "PGOHUM00000289731"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOHUM00000289731"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOHUM00000289731"; level 3; tag "2way_pseudo_cons"; yale_id "PGOHUM00000289731"; ucsc_id "NM_000987.3-9"; parent_id "ENSG00000161970";
chr10   Yale_UCSC       transcript      6071517 6071921 .       -       .       gene_id "PGOHUM00000289732"; transcript_id "PGOHUM00000289732"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOHUM00000289732"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOHUM00000289732"; level 3; tag "2way_pseudo_cons"; yale_id "PGOHUM00000289732"; ucsc_id "NM_000994.3-10"; parent_id "ENSG00000144713";
chr10   Yale_UCSC       transcript      6293104 6294274 .       -       .       gene_id "PGOHUM00000289733"; transcript_id "PGOHUM00000289733"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOHUM00000289733"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOHUM00000289733"; level 3; tag "2way_pseudo_cons"; yale_id "PGOHUM00000289733"; ucsc_id "NM_001007070.1-2"; parent_id "ENSG00000137575";
chr10   Yale_UCSC       transcript      7295121 7295279 .       -       .       gene_id "PGOHUM00000289735"; transcript_id "PGOHUM00000289735"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOHUM00000289735"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOHUM00000289735"; level 3; tag "2way_pseudo_cons"; yale_id "PGOHUM00000289735"; ucsc_id "NM_004374.3-4"; parent_id "ENSG00000164919";

How do I convert the gene_id (e.g PGOHUM00000289731) to HGNC symbols? Biormart and BioDBnet do not seem to offer this

genecode pseudogene gene • 1.2k views
ADD COMMENTlink modified 3.8 years ago by Ashis90 • written 3.8 years ago by biocyberman760
1
gravatar for Ashis
3.8 years ago by
Ashis90
Baltimore, USA
Ashis90 wrote:

You can probably download the complete HGNC dataset (ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt). Here the "pseudogene.org" column contains gene ids similar to your ones. You might want to write a small program to get corresponding hgnc symbols.

ADD COMMENTlink written 3.8 years ago by Ashis90

The answer did not point exactly to what I was looking for, but it is sufficient to get me there. The file I need to download is this one: ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/locus_groups/pseudogene.txt

ADD REPLYlink written 3.8 years ago by biocyberman760
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