Table 1. CC3D parameters that were varied in the model and their biological significance in branching morphogenesis and cleft formation.

CC3D parameters to vary	Biological effect simulated	Experimental data - Effect seen in cleft formation	Unknown biological effects
Focal point plasticity λ (FPP λ)	Actin-myosin contractility in the cleft cells	Decreasing contractility prevents initiated clefts from progressing [6]	Increasing contractility.Increasing or decreasing contractility within cleft region
Mitosis rate (MR)	Epithelial cell proliferation – in outer columnar cells (OCC) and inner polymorphic cells (IPC)	Decreasing cell proliferation in the whole organ decreased cleft progression but not initiation [6]	Increasing mitosis rate.Varying mitosis rates in specific subsets of cells in OCC and IPC populations.
Cell-cell (CC) contact energy	E-cadherin-based cell-cell junctions	E-cadherin mRNA was found to be ∼6 fold lower in the cleft epithelium than in the bud epithelium [10] Global reduction of E-cadherin decreases branching morphogenesis [38]	Increasing E-cadherin protein activity.Increasing or decreasing E-cadherin levels in the cleft region
Cell-matrix (CM) contact energy	Cell-matrix adhesions	Decreased FN decreases cleft formation [5]. Lower FN assembly reduces cleft depth [22]	Increasing FN assembly levels in the cleft region