ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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Cannot find interaction in annotated db #46

Closed parkjooyoung99 closed 10 months ago

parkjooyoung99 commented 2 years ago

I was trying to find more information about this interaction so I have visited InnateDB (https://www.innatedb.com/index.jsp) but could not find this interaction. i wonder if our interaction.csv is well updated.

image

Also, i wonder with what rationale have you annotated some interactions.

Thank you :)

https://www.innatedb.com/interactionSearch.do?listType=interaction&participantField=idphysical_molecule&participantKeyword=38333&participantKeywordExact=true https://www.innatedb.com/interactionSearch.do?listType=interaction&participantField=idphysical_molecule&participantKeyword=77290&participantKeywordExact=true

luzgaral commented 2 years ago

Hi, I see HLA-c self interaction here https://www.innatedb.com/interactionSearch.do?listType=interaction&participantField=idphysical_molecule&participantKeyword=77290&participantKeywordExact=true

parkjooyoung99 commented 2 years ago

Thanks for fast reply!

However, i have already checked the link and still could not find HLA-C:FAM3C interaction.

luzgaral commented 2 years ago

Apologies for the late reply.

We retrieved InnateDB-all data from http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE# This seems to be in InnateDB from https://thebiogrid.org/interaction/2263751

Please, note that we have not curated this interaction, as it does not appear as "curated".

Best,

Luz