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Duplicated POMC/b-Endorphin_byPOMC interactions #6

Open dnjst opened 1 year ago

dnjst commented 1 year ago

Congratulations on cellphonedb v4.1 and all the new curation!

A colleague and I were going over it, and it seems in the latest database, 3 of the interactions are present twice, once as a peptide->peptide and once as a complex->peptide where the complex only contains the POMC gene P01189

b-Endorphin_byPOMC  P41143
b-Endorphin_byPOMC  P35372
b-Endorphin_byPOMC  P41145
...
P01189  P41143
P01189  P41145
P01189  P35372
ktroule commented 1 year ago

Thanks for pointing this out, we will amend it.

Kind regards.

luzgaral commented 1 year ago

Hi @dnjst

Thank you for pointing this out.

POMC/P01189 (or pro-opiomelanocortin) is a precursor of a variety of ligands, including b-Endorphin, α-melanocyte-stimulating hormone or corticotropin. This is why it was included both as general precursor but also as b-Endorphin. So, although they look redundant in the way they are coded in our database, they represent different biology. We will work on a way to standarise these cases so that don't cause technical redundancy.

On a side note, all non-protein ligands are coded as complexes in CellphoneDB. This is to allow the inclusion of all the key enzymes in their biosynthetic pathway, even if n=1.

Hope this helps to clarify the issue.

Best

Luz