Antibody Matching Transcripts

Question

[science03]

Hello everyone, I am interested to find the matching isoforms of a gene that my HPA antibody is able to hit. When I check the Human Atlas Protein website it gives me a list of 4 transcripts my antibody can recognize. However, when I open ensembl and I check the general identifiers page there are some extra transcripts that ensembl claims to be recognized by the antibody. I don't really know where to go from here; Should I take into consideration the list that Human Protein Atlas is providing or the information on Ensembl would be more accurate?

Thank you in advance!

Answer 1

[Ben Moore]

Hi Science03,

The 'General Identifiers' page in the transcript tab in Ensembl provides links to external databases that map to that transcript. More information on the mapping to external databases that we perform can be found here: http://www.ensembl.org/info/genome/genebuild/xrefs.html

Ensembl does not perform any antibody mapping for proteins encoded by the transcripts annotated in our database. I'm not sure which page you are viewing in Ensembl, but other transcripts that you find on that page (in the table at the top of the page?) are the other alternative transcripts of that gene. You can click on the stable ID for each transcript and view the General Identifiers for each transcript within its own transcript tab.

E.g. http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000139618;r=13:32315086-32400268;t=ENST00000380152

Best wishes

Ben

[science03]

Hello Ben, Thank you for taking the time to reply to my post. I understand that for each different isoform of a specific gene you can access the "general identifiers" and that's the strategy I have followed.

However, under the General Identifiers tab there is an option (external reference) for Human Protein Atlas (HPA) ; As far as I understood, the HPA section can tell us which specific antibody is able to hit each one of the isoforms. So basically from Ensembl I retrieve the information that : Isoform "X" is hit by Antibody "Y". To confirm this, I check the official Human Protein Atlas Webpage and according to that ,Antibody "Y", is in fact not matching the isoform "X" which I had previously identified in Ensembl. That's why I am facing a dilemma on how to proceed next and which information to consider as more reliable. I hope you will be able to shed a little bit of light in this confusing situation. Thank you in advance!

[Ben Moore]

No problem- very happy to help.

The links found on the General Identifiers page are based on mappings between features in external bases and those in Ensembl. For the Human Protein Atlas, these links are imported directly from mappings performed by HPA. The HPA identifiers are mapped to Ensembl IDs according to the following file: https://www.proteinatlas.org/download/xref.php

The BRCA2 peptide, ENSP00000369497 (ENST00000380152), is mapped to the HPA ID, HPA026815. This is reflected on the General Identifiers page in Ensembl: http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000139618;r=13:32315086-32400268;t=ENST00000380152

HPA026815 is the HPA entry for the BRCA2 gene, which contains information about two Ensembl transcripts, including ENST00000380152: https://www.proteinatlas.org/ENSG00000139618-BRCA2

I think the issue may be that you are using Ensembl to 'retrieve the information that : Isoform "X" is hit by Antibody "Y".', but the mapping is between an Ensembl peptide/transcript and an HPA gene feature.

However, I'm not sure if there is a discrepancy between the links in Ensembl and HPA. Can you provide links to the Ensembl and HPA pages where you see this?

I would also suggest getting in touch with HPA to get further details about the mapping process: https://www.proteinatlas.org/about/contact