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Teichlab / cellphonedb

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why cellphonedb still enriches some interactions even this cluster cells don't expression genes of receptor/ligand #210

Open hua1991 opened 3 years ago

hua1991 commented 3 years ago

When I use my single-cell sequencing data to analyze the interaction of cells, I found one cluster enriched "IL1 receptor-IL1B" and showed significant p-value. But I checked the raw data of IL1R1(receptor) and IL1B (ligand) gene expression in my single-cell sequencing data, and all this kind of cluster cells don't express Il1r1 and Il1b. I thought cellphonedb to enrich the interaction between two clusters was based on the genes (receptor and ligand) expression. Does anyone know why it can enrich this interaction in my data?

mief commented 3 years ago

This should not happen. The corresponding ligand and receptor should be expressed at least above the specified threshold? Il1 receptor is a complex, are both genes expressed in the cluster? Can you send us your data and we can check?