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Teichlab / cellphonedb

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Unexpected interaction HLADPB1-NRG1 (also not found in the cited source database) #233

Closed MaxKman closed 3 years ago

MaxKman commented 3 years ago

Dear cellphonedb team,

thanks for providing and maintaining such a great resource. In one of the analysis I performed with cellphonedb the following interaction came up: HLADPB1 - NRG1

I found this interaction surprising (from a biological point of view) so I tried to look it up in the literature but couldn't find anything. In cellphonedb the source for this interaction is noted as 'InnateDB-All'. However, I also couldn't find this interaction listed at https://www.innatedb.com/

Can you still trace where it came from? I thought I bring this up in case there is a systematic problem causing this (and potentially other false entries). Of course it might just come from an older version of innatedb.

Thanks!

Best, Max

MaxKman commented 3 years ago

Hey again,

After looking a bit further here are some more examples of HLA interactions which seem to have the same problem: HLA-C - FAM3C (CPI-SS034D36D2F) HLADQB2 - PRL (CPI-SS026776C89) HLADPA1 - TNFL9 (CPI-SS028784FC6)

would be good to now what is going on there, also because these interactions make there way into the literature (e.g. HLA-C/FAM3c in https://www.nature.com/articles/s41467-020-16164-1.pdf?origin=ppub).

I hope it's just some misunderstanding on my side!

Best, Max

rvento commented 3 years ago

Dear Max,

Thank you for pointing this out. The interaction is available at https://psicquic.all.innatedb.com/webservices/current/search/query/species:human . Still, we strongly encourage our users to rather use the curated interactions.

Best,

Roser