Question about update CellChatDB by adding user-defined ligand-receptor pairs

[makabakayu]

Hi CellChat team,

I am trying to use only the ligand-receptor pairs specified by myself, so I have to give up using the original CellChatDB, but there is no cofactor and complex in my ligand-receptor pairs, only ligand and receptor information. Will this affect the use of this function? Do I still need to create two empty CSV files for complex and cofactor?

Best, Zhiyu

[sqjin]

@makabakayu No need to add these additional information or files. Please check our toturial on how to update the database using the updateCellChatDB

[makabakayu]

@makabakayu No need to add these additional information or files. Please check our toturial on how to update the database using the updateCellChatDB

Thanks for your quick reply. Sorry, I didn't make it clear. I mean if I don't need the complex and cofactor file information, can I delete the contents of these two files, which means CellChatDB$complex and CellChatDB$cofactor will be empty, and the interaction file only has my own ligand receptor pairs. Will this affect the use of this function?

[sqjin]

@makabakayu No, this will not affect the analysis and you can still run cellchat. We have a tutorial on this part.

[makabakayu]

@sqjin Thanks for the reply. I followed the tutorial but there was an error when running the subsetData(cellchat): Issue identified!! Please check the official Gene Symbol of the following genes: CARNMT1_CARNS1_CNDP2 APRT_HPRT1_MTAP_PNP_LACC1 ACSM2A_ACSM5_ACSF2_ACSM3_UGT1A1_ACSM2B_ACSM1_ACSM4 SIAE_PON2_ASPG_ACHE_ASPA_AMDHD2_ALDH7A1_ACOT12_CES2_ALDH1A3_PAFAH1B2_ALDH3B1_ACYP1_HMGCL_PON3_IAH1_ESD_PAFAH1B3_ACY1_ALDH3A1_PAFAH2_PIGL_UGT1A1_ACSS1_ALDH3B2_ALDH1B1_ACY3_CES1_CYP17A1_ACSS3_PLA2G7_MACROD2_ALDH2_ALDH3A2_ABHD14A-ACY1_ACSS2_ACYP2_ALDH9A1_HMGCLL1_MACROD1_PON1

In my own receptor ligand pairs, most of my ligand or receptor are made up of multiple genes. Why can't it identify every gene? Is the format wrong?

[sqjin]

@makabakayu In your case with mutiple subunits, you have to provide the complex information to clarify the genes/subunits contained in each ligand and receptor.