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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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questions about cellphonedb database protien_input file #120

Closed YinCY123 closed 7 months ago

YinCY123 commented 1 year ago

Hello! First of all thanks for this great work!

I'm reading the CellphoneDB's documentation, and I find in the protein_input section c, it's said that the membrane and secreted proteins are not considered for the cell-cell communication analysis.

what if I want to include those proteins in my analysis? Just convert False to True or True to False in the other column? Is there any change that I need to do?

thanks for your reply!

ktroule commented 1 year ago

Hi.

Sorry, I think the description in the documentation is a little bit misleading, here you have a better explanation from the paper and refer to the original implementation.

Others. We created another column named ‘others’ that consists of membrane and secreted proteins that are excluded from our cell–cell communication analysis because they are not directly involved in the recognition of the ligand (e.g., co-receptors) or they require more specialized annotation (e.g., nerve-specific receptors such as those related to ear binding, olfactory receptors, taste receptors and salivary receptors). In addition, we excluded small-molecule receptors, immunoglobulin chains and viral and retroviral proteins, pseudogenes, cancer antigens and photoreceptors. We also added ‘others_desc’ to allow a brief description of the excluded protein.

We will review the code and get back to you, but nowadays all proteins are used so no filter should apply based on this.

Regards

YinCY123 commented 1 year ago

OK, thanks for your time!