Some Ensp Ids Not Converting To Hgnc Symbol In Biomart

Question

[ismeet.kaur]

I am not able to convert some of the ENSP IDs to HGNC symbol using Biomart, but when searching for those IDs in Ensembl database they are assigned a gene ID as well as transcript ID. Following are some of these ENSP IDs:

ENSP00000007633
ENSP00000008311
ENSP00000023165
ENSP00000160874
ENSP00000172196
ENSP00000190839
ENSP00000193422
ENSP00000194097

Please let me know how to convert them.

Answer 1

[Neilfws]

You did not mention the species, but when I search Google for ENSP00000007633, I see that these are human proteins.

My search takes me to this page, which informs me that:

• the entry has been "Retired"
• the Latest Version is ENSP00000007633.7
• the Ensembl Release is 57

Therefore, I need to visit the Ensembl archives page, follow the link for release 57, then the link to BioMart for release 57.

Using the ENSP IDs as filters to fetch the HGNC symbol attribute, we get:

Ensembl Gene ID    Ensembl Transcript ID    HGNC symbol
ENSG00000006534    ENST00000007633          ALDH3B1
ENSG00000010539    ENST00000008311          ZNF200
ENSG00000021602    ENST00000023165          KLRA1
ENSG00000075218    ENST00000160874          GTSE1
ENSG00000064195    ENST00000172196          DLX3
ENSG00000206239    ENST00000190839
ENSG00000081177    ENST00000193422          EXD2
ENSG00000081770    ENST00000194097          NAIP

However, you need to investigate the reason(s) for the retirement of these IDs.

[ismeet.kaur]

It works thanks!

[ismeet.kaur]

@Neilfws If we face similar problem with Entrez IDs then what do we do? For example following IDs:

100113377
100127919
100128009
100128034
100128046
100128256
100128435
100128500
100128542

Then where to search?

[Neilfws]

You need to search the Entrez Gene database - http://www.ncbi.nlm.nih.gov/gene. I note for example that the first of those has again, been retired and replaced with a new ID.

[ismeet.kaur]

@Neilfws how to extract HGNC ids from Entrez gene batch search options??

[Neilfws]

Just paste all the IDs in the search box, separated by space or comma. Also, read about EUtils.