I don't know anything about these proteins, but if you want to see how they're related, you should be able to click the lines between proteins on the STRING plot, and it'll give you all the evidence it based the relationships on.
Genetics: Chromosome 6 BTN2A2 and BTN3A3
- Thread starter Hutan
- Start date
jnmaciuch
Senior Member (Voting Rights)
If you select the BNT2A2 node you can go to the “Edges” tab and get details about the connection. Here is seems that the connection is just driven by both being mentioned in abstracts together, in the specific context of milk secretion:
Andy
Senior Member (Voting rights)
Butyrophilin 2A2 promotes T cell immunoregulation via CD45 phosphatase activation and protects against murine autoimmune glomerulonephritis and pregnancy loss, 2025, Karumanchi et al
Open access
Open access
ChronicallyOverIt
Senior Member (Voting Rights)
Perusing therapies for antagonism of BTN3A and saw this:
www.imchecktherapeutics.com
About ICT01
Imcheck Therapeutics : Opening new spaces in Immuno-Oncology.
www.imchecktherapeutics.com
I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread.
Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of the traits, since a variant can be significant just because it is correlated to (in LD with) another variant which is actually causal.
Here are traits associated with rs9358913/6:26239176:A:G (the lead DecodeME variant near BTN2A2). This is just the 20 most significant:
The trait most significantly associated with this variant is expression of the HIST1H2BD gene.
The G allele at this variant is associated with increased risk of ME/CFS (odds ratio greater than 1/beta greater than 0 in DecodeME) and decreased expression of HIST1H2BD (beta less than 0 above).
----
There were too many traits associated at p<1e-6 to include them all in the post, so I'll just attach a spreadsheet that has all traits associated with the 8 DecodeME variants.
Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of the traits, since a variant can be significant just because it is correlated to (in LD with) another variant which is actually causal.
Here are traits associated with rs9358913/6:26239176:A:G (the lead DecodeME variant near BTN2A2). This is just the 20 most significant:
The trait most significantly associated with this variant is expression of the HIST1H2BD gene.
The G allele at this variant is associated with increased risk of ME/CFS (odds ratio greater than 1/beta greater than 0 in DecodeME) and decreased expression of HIST1H2BD (beta less than 0 above).
----
There were too many traits associated at p<1e-6 to include them all in the post, so I'll just attach a spreadsheet that has all traits associated with the 8 DecodeME variants.
I posted on the CA10 thread about a website called Open GWAS / Genotype-Phenotype Map, where you can upload summary stats, and it tests for colocalization (testing if traits share a causal variant) of the uploaded trait with thousands of other GWAS traits and millions of molecular traits.
I thought it'd be worth copying traits identified as potentially colocalizing with ME/CFS at other loci onto the forum, just in case they may be important.
These are the traits that show evidence of colocalization with ME/CFS at the chr6p22.2 locus (near BTN2A2):
I thought it'd be worth copying traits identified as potentially colocalizing with ME/CFS at other loci onto the forum, just in case they may be important.
These are the traits that show evidence of colocalization with ME/CFS at the chr6p22.2 locus (near BTN2A2):
ScoutB
Senior Member (Voting Rights)
Do you have any thoughts on the fact that this GWAS comparison technique seems to often be suggesting different genes (as having their expression altered) for each variant than the ones originally identified? E.g. at this variant we have been thinking about BTN2A2 and BTN3A3, but it looks like the Open GWAS comparison might be pointing more towards H4C8, if I'm understanding correctly?
I guess GTEx has the advantage of being tissue-specific (though maybe the con of being an autopsy study)? While the GWAS studies going into this Open GWAS system seem to be looking at gene expression in the blood of living people? I assume the GWAS studies also tend to have more samples than GTEx did?
I guess GTEx has the advantage of being tissue-specific (though maybe the con of being an autopsy study)? While the GWAS studies going into this Open GWAS system seem to be looking at gene expression in the blood of living people? I assume the GWAS studies also tend to have more samples than GTEx did?
Yes, but this region on chromosome 6 has a large number of genes densely packed together, so I think it's plausible that a variant can affect multiple genes here. A variant could very well be directly affecting one gene, which in turn affects another gene, and both would show up as associated with the variant.
I think GTEx is actually one of the data sources used for their website. So it is interesting that DecodeME identified 7 genes' eQTLs that colocalize with ME/CFS at this locus, but none of them showed up here, while another gene, H4C8, did.
Edit: Just noticed LocusZoom doesn't show all genes if there are too many. Here are all the genes near the locus, showing how dense it is:
Last edited: