Table 1. Top differential cell type interactions identified by CINS for the IPF dataset.

The IPF-Control column lists the difference in the number of times the edge between the two cells was identified in 100 bootstrap runs for each of the two datasets. Negative values indicate that it was identified more for the Control whereas positive numbers mean that the interaction is more prevalent in IPF. For all listed edges the interaction was only identified in one of the two datasets (score of 100 or -100).

cell_type1	cell_type2	IPF-Control	Reference
Macrophage	Ciliated	-100	There is strong interaction between ciliated cell and Macrophage in COVID-19 critical cases [44]
Fibroblast	Lymphatic	-100	Fibroblast produce extracellular matrix which is critical to lymph node microenvironment [45]
cDC2	DC_Mature	100
cDC2	cDC1	-100	cDC2 and cDC1 are cross-talking with each other [23]
Macrophage	cDC1	100
Mesothelial	Aberrant_Basaloid	100
Macrophage_Alveolar	pDC	-100	Macrophage_Alveolar (AM) and pDC are involved in antiviral immune, and pDC will be activated if the AM defense line is broken [46]
Myofibroblast	VE_Venous	-100	Injury lets endothelial cells transform to myofibroblast [47]
Ciliated	ncMonocyte	-100	Ciliated cells may contribute to monocyte inflow in COVID-19 [44]
Multiplet	VE_Capillary_B	100
B_Plasma	Mesothelial	-100	Excess plasma cells are found with mesothelial cells on effusion cytology smear [48]
VE_Capillary_B	SMC	-100
Pericyte	SMC	100	Brain pericytes and vascular SMC comprise mural cells which is important to support blood vessels [49]
ncMonocyte	Multiplet	100
ncMonocyte	DC_Mature	-100
T_Regulatory	Fibroblast	100	Treg cell regulates fibroblast in lung [22]
VE_Arterial	VE_Venous	100
T	T_Regulatory	100
VE_Peribronchial	Pericyte	100	One pericyte can communicate with more than one endothelial cells [50]
T_Regulatory	DC_Langerhans	-100