About the communication direction

[yewero]

In the pvalues.txt file, if the "receptor_a" is True and "receptor_b" is False, as follows:	interacting_pair	gene_a	gene_b	receptor_a	receptor_b	X cell\	Y cell
A_B	A	B	True	False	0

Does this mean that X cell is the sending cell which could express the receptor gene A? I am confused about that.

[mief]

Hi, In addition to ligand-receptor interactions, we include also receptor-receptor interactions and that's why we did not include any directionality of the interactions. However, like you said, we included the information whether a protein is a receptor, so in this case you can use that to detect the sending/receiving cell. To help with this, we included additional information about some of the ligands in the 'secreted_desc' field, whether they are cytokines, growth factors or hormones.

[yewero]

This script fixOrder.py could simply fix the order of gene pairs in the output.

[lixin4306ren]

Hi, @yewero

In some cases, receptor_a and receptor_b are both FALSE, how do you determine the direction in these situations? Thanks.

Xin

[yewero]

@lixin4306ren The script fixOrder.py will only change the order from receptor/ligand to ligand/receptor. For the cases where receptor_a and receptor_b are both FALSE, the order will not be changed.