Table 1 Total input to activity (omega, ω) functions for each protein in the network.
From: Computational evidence for multi-layer crosstalk between the cadherin-11 and PDGFR pathways
Omega | Function | Explanation |
|---|---|---|
\({\omega }_{cdh11}\) | \(\left(\frac{1.0 + {\alpha }_{cdh{11}_{b{y}_{c}}}}{{\alpha }_{cdh{11}_{b{y}_{c}}}}\right)\cdot \left(\frac{c \cdot {\alpha }_{cdh{11}_{b{y}_{c}}}}{1.0 + (c \cdot {\alpha }_{cdh{11}_{b{y}_{c}}})}\right)\) | Total input to the activity of cadherin-11 |
\({\omega }_{pdgfrA}\) | \(\left(\frac{1.0 + {\alpha }_{{pdgfrA}_{{by}_{a}}}+{\alpha }_{{pdgfrA}_{{by}_{c}}}}{ {\alpha }_{{pdgfrA}_{{by}_{a}}}+{\alpha }_{{pdgfrA}_{{by}_{c}}}}\right)\cdot \left(\frac{a\cdot {\alpha }_{{pdgfrA}_{{by}_{a}}}+c \cdot {\alpha }_{{pdgfrA}_{{by}_{c}}} }{1.0 + \left( a\cdot {\alpha }_{{pdgfrA}_{{by}_{a}}}+ c\cdot {\alpha }_{{pdgfrA}_{{by}_{c}}}\right)}\right)\) | Total input to the activity of PDGFR-α |
\({\omega }_{pdgfrB}\) | \(\left(\frac{1.0 + {\alpha }_{{pdgfrB}_{{by}_{b}}}}{ {\alpha }_{{pdgfrB}_{{by}_{b}}}}\right)\cdot \left(\frac{b\cdot {\alpha }_{{pdgfrB}_{{by}_{b}}}}{1.0 + b\cdot {\alpha }_{{pdgfrB}_{{by}_{b}}} }\right)\cdot \left(1-\left(\frac{1+ {\beta }_{pdgf{rB}_{b{y}_{cdh11}}}}{{\beta }_{pdgf{rB}_{b{y}_{cdh11}}}}\right)\cdot \left(\frac{{\beta }_{pdgf{rB}_{b{y}_{cdh11}}}\cdot cdh11}{1+{(\beta }_{pdgf{rB}_{b{y}_{cdh11}}}\cdot cdh11)}\right)\right)\) | Total input to the activity of PDGFR-β |
\({\omega }_{ras}\) | \(\left(\frac{1.0+{\alpha }_{ra{s}_{b{y}_{pdgfrA}}}+{\alpha }_{ra{s}_{b{y}_{pdgfrB}}}}{{\alpha }_{ra{s}_{b{y}_{pdgfr}}}+{\alpha }_{ra{s}_{b{y}_{pdgfrB}}}}\right)\cdot\) \(\left(\frac{pdgfrA\cdot {\alpha }_{ra{s}_{b{y}_{pdgfrA}}}+pdgfrB\cdot {\alpha }_{ra{s}_{b{y}_{pdgfrB}}}}{1.0 + \left(pdgfrA\cdot {\alpha }_{ra{s}_{b{y}_{pdgfrA}}}\right)+\left(pdgfrB\cdot {\alpha }_{ra{s}_{b{y}_{pdgfrB}}}\right)}\right)\) | Total input to the activity of RAS |
\({\omega }_{raf}\) | \(\left(\frac{1.0+{\alpha }_{ra{f}_{b{y}_{ras}}}}{{\alpha }_{ra{f}_{b{y}_{ras}}}}\right)\cdot \left(\frac{ras\cdot {\alpha }_{ra{f}_{b{y}_{ras}}}}{1.0+(ras\cdot {\alpha }_{ra{f}_{b{y}_{ras}}})}\right)\) | Total input to the activity of RAF |
\({\omega }_{mek}\) | \(\left(\frac{1.0+{\alpha }_{me{k}_{b{y}_{raf}}}}{{\alpha }_{me{k}_{b{y}_{raf}}}}\right)\cdot \left(\frac{raf\cdot {\alpha }_{me{k}_{b{y}_{raf}}}}{1.0+(raf\cdot {\alpha }_{me{k}_{b{y}_{raf}}})}\right)\) | Total input to the activity of MEK |
\({\omega }_{erk}\) | \(\left(\frac{1.0+{\alpha }_{er{k}_{b{y}_{mek}}}}{{\alpha }_{er{k}_{b{y}_{mek}}}}\right)\cdot \left(\frac{mek\cdot {\alpha }_{er{k}_{b{y}_{mek}}}}{1.0+(mek\cdot {\alpha }_{er{k}_{b{y}_{mek}}})}\right)\cdot \left(1-\left(\frac{1+{\beta }_{{erk}_{b{y}_{dusp1}}}}{{\beta }_{{erk}_{b{y}_{cdusp1}}}}\right)\cdot \left(\frac{{\beta }_{{erk}_{b{y}_{dusp1}}}\cdot dusp1}{1+({\beta }_{{erk}_{b{y}_{dusp1}}}\cdot dusp1)}\right)\right)\) | Total input to the activity of ERK |
\({\omega }_{dusp1}\) | \(\left(\frac{1.0+{\alpha }_{{dusp1}_{{by}_{erk}}}}{{\alpha }_{{dusp1}_{{by}_{erk}}}}\right)\cdot \left(\frac{erk\cdot {\alpha }_{{dusp1}_{{by}_{erk}}} }{1.0+\left(erk\cdot {\alpha }_{{dusp1}_{{by}_{erk}}}\right)}\right)\cdot \left(1-\left(\frac{1+{\beta }_{{dusp1}_{b{y}_{Bcat}}}}{ {\beta }_{{dusp1}_{b{y}_{Bcat}}}}\right)\cdot \left(\frac{ Bcat\cdot {\beta }_{{dusp1}_{b{y}_{Bcat}}}}{1+\left(Bcat\cdot {\beta }_{{dusp1}_{b{y}_{Bcat}}}\right)}\right)\right)\) | Total input to the activity of DUSP1 |
\({\omega }_{Bcat}\) | \(1-\left(\frac{1+{\beta }_{Bca{t}_{b{y}_{cdh11}}}}{ {\beta }_{Bca{t}_{b{y}_{cdh11}}}}\right)\cdot \left(\frac{cdh11\cdot {\beta }_{Bca{t}_{b{y}_{cdh11}}}}{1+\left(cdh11\cdot {\beta }_{Bca{t}_{b{y}_{cdh11}}}\right)}\right)\) | Total input to the activity of β-catenin |
\({\omega }_{cyclinD1}\) | \(\left(\frac{1.0+{\alpha }_{{cyclinD1}_{b{y}_{dusp1}}}}{{\alpha }_{{cyclinD1}_{b{y}_{dusp1}}}}\right)\cdot \left(\frac{dusp1\cdot {\alpha }_{{cyclinD1}_{b{y}_{dusp1}}}}{1.0+(dusp1\cdot {\alpha }_{{cyclinD1}_{b{y}_{dusp1}}})}\right)\) | Total input to the activity of Cyclin-D1 |
