Table 2 Parameter values used to populate the omega functions in Table 1 in the baseline simulation.
From: Computational evidence for multi-layer crosstalk between the cadherin-11 and PDGFR pathways
Parameter | Value | Explanation |
|---|---|---|
\(c\) | 0.1 | Initial cell–cell adhesion via the cadherin-11 on the adjacent cell. Value adjusted using Madarampalli et al., 2019 |
\(a\) | 0.1 | Initial PDGF-A ligand activity. Value adjusted using Madarampalli et al., 2019 and Passanha et al., 2022 |
\(b\) | 0.4 | Initial PDGF-B ligand activity. Value adjusted using Madarampalli et al., 2019 and Passanha et al., 2022 |
\(Bcat\) | 1 | Initial β-catenin activity |
h | 1 | Gain value of all omega (ω) functions |
\({k}_{i}\) | 1 | General decay parameter |
\({k}_{iB}\) | 2 | Decay parameter for β-catenin activity |
\({\alpha }_{cdh{11}_{b{y}_{c}}}\) | 1 | Activation of cadherin-11 by cell–cell adhesion \((c)\) |
\({\alpha }_{{pdgfrA}_{{by}_{a}}}\) | 0.5 | Activation of PDGFR-α by PDGF-α ligand. Value adjusted using Madarampalli et al., 2019 and Passanha et al., 2022 |
\({\alpha }_{{pdgfrA}_{{by}_{c}}}\) | 0.5 | Activation of PDGFR-α by extracellular cadherin-11 binding. Value adjusted using Madarampalli et al., 2019 and Passanha et al., 2022 |
\({\alpha }_{{pdgfrB}_{{by}_{b}}}\) | 0.5 | Activation of PDGFR-β by PDGF-β ligand. Value adjusted using Madarampalli et al., 2019 and Passanha et al., 2022 |
\({\beta }_{pdgf{rB}_{b{y}_{cdh11}}}\) | 1 | Inhibition of PDGFR-β by same-cell cadherin-11 |
\({\alpha }_{ra{s}_{b{y}_{pdgfrA}}}\) | 1 | Activation of RAS by PDGFR-α |
\({\alpha }_{ra{s}_{b{y}_{pdgfrB}}}\) | 1 | Activation of RAS by PDGFR-β |
\({\alpha }_{ra{f}_{b{y}_{ras}}}\) | 1 | Activation of RAF by RAS |
\({\alpha }_{me{k}_{b{y}_{raf}}}\) | 1 | Activation of MEK by RAF |
\({\alpha }_{er{k}_{b{y}_{mek}}}\) | 1 | Activation of ERK by MEK |
\({\beta }_{{erk}_{b{y}_{dusp1}}}\) | 1 | Inhibition of ERK by DUSP1 |
\({\alpha }_{{dusp1}_{{by}_{erk}}}\) | 1 | Activation of DUSP by ERK |
\({\beta }_{{dusp1}_{b{y}_{Bcat}}}\) | 1 | Inhibition of DUSP by β-catenin |
\({\beta }_{Bca{t}_{b{y}_{cdh11}}}\) | 1 | Inhibition of β-catenin by cadherin-11 |
\({\alpha }_{{cyclinD1}_{b{y}_{dusp1}}}\) | 1 | Activation of Cyclin-D1 by DUSP1 |
