5.1) Table 5: Parameters in the ten-gene regulatory network (p = proteins, t = transcripts, m = molecules, c = cell) [11, 42-45].
| Parameter | Value with units | value with units |
|---|---|---|
| Transcription rate constant | t/p/minute | 1/second |
| kRPA, kRPC, kRPD, kRPF, kRC2PG, kRPJ, kRC2PK | 7.3×10-4 | 1.22×10-5 |
| kRAPA, kRAF2PB, kRAPC, kRF2PD, kRC2F2PD, KREQPF, kRPG, kRK2PJ, kRPK | 7.3×10-1 | 1.22×10-2 |
| kRPE, kRPH | 4.2×10-3 | 7×10-5 |
| KRPB | 3.6×10-4 | 6×10-6 |
| KRAPB | 3.6×10-2 | 6×10-4 |
| kRF2PB | 3.6×10-1 | 6×10-3 |
| kRD2PC, kRC2PD | 0 | 0 |
| kRAD2PC | 7.3×10-2 | 1.22×10-3 |
| kRD2PE | 4.2×10-7 | 7×10-9 |
| Transcript degradation rate constant | 1/minute | 1/second |
| kDMA, kDMC, kDMD, kDMF, kDMG, kDMK | 3.1×10-2 | 5.1×10-4 |
| KDMB | 1.1×10-2 | 1.8×10-4 |
| kDME | 1.4×10-3 | 2.3×10-5 |
| kDMH | 4.8×10-4 | 8×10-6 |
| kDMJ | 9.7×10-3 | 1.62×10-4 |
| Translation rate constant | p/t/minute | 1/second |
| KTA, kTC, kTD, kTF, kTG, kTK | 2.5 | 4.17×10-2 |
| KTB | 1.2 | 2×10-2 |
| KTE, kTH | 18.9 | 3.15×10-1 |
| KTJ | 24.5 | 4.08×10-1 |
| Protein degradation rate constant | 1/minute | 1/second |
| KDA, kDC, kDegD, kDF, kDG, kDK | 6.6×10-3 | 1.1×10-4 |
| KDB | 2.9×10-3 | 4.83×10-5 |
| KDE | 7.8×10-4 | 1.3×10-5 |
| KDH | 1.6×10-4 | 2.67×10-6 |
| KDJ | 7.7×10-3 | 1.28×10-4 |
| Dimer association rate constant | c/m/minute | 1/ (nM * sec) |
| kC2, kD2, kF2, kG2, kK2, kAB | 5.9×10-3 | 7.4×10-3 |
| KEQ | 2.4×10-3 | 3×10-3 |
| Dimer dissociation rate constant | 1/minute | 1/second |
| kUC2, kUD2, kUF2, kUG2, kUK2, kUAB | 3.8 | 6.3×10-2 |
| KUEQ | 3.6 | 6×10-2 |
| Dimer degradation rate | 1/minute | 1/second |
| kDC2, kDD2, kDF2, kDEQ, kDG2, kDK2, kDAB | 6.6×10-3 | 1.1×10-4 |
| Promoter-transcription factor association rate constant | c/m/minute | 1/ (nM * sec) |
| kPA, kPB, kPC, kPD, kPG, kPK, kPE, kPF, kPH, kPJ | 7.5×10-4 | 9.4×10-4 |
| Promoter-transcription factor dissociation rate constant | 1/minute | 1/second |
| kUPA, kUPB, kUPC, kUPD, kUPG, kUPK, kUPE, kUPF, kUPH, kUPJ | 0.39 | 6.5×10-3 |
Ligand concentration, Q = 2 molecules/cell or 2.66×10-2 nM
Total number of promoters per gene, PT = 2
Avogadro’s number: 6.02*1023 molecules/mole
Assumed cell volume: 125 μm3/cell = 125*10-18 m3/cell = 1.25*10-13 Liters/cell since 1M = 1 mole/Liter, 1 cell/ (molecule*minute) = 1.2542*109 1/ (M*sec)