Table 2.
Counts of the occurrence of parameters in dominant terms of phenotypes that yielded limit cycles for model Design 3 through Design 9.
| Design # | αxy | αyy | αxz | αyz | αzz | γyx | γzx | γyy | γzy | γzz | K | δ | ε | βx | βy | βz | βs | vy | vz |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 0 | *6 | 0 | *6 | 1 | 1 | #5 | 1 | 4 | 0 | – | ‡7 | 3 | 1 | 0 | 4 | 0 | 1 | 0 |
| 4 | *41 | 23 | 1 | 17 | *48 | 12 | 20 | 12 | 18 | 4 | †54 | ‡46 | ‡63 | 14 | 11 | 5 | 0 | 2 | 0 |
| 5 | 3 | *12 | 2 | *10 | 4 | 0 | #11 | 0 | #13 | 0 | 8 | ‡14 | ‡12 | 5 | 1 | 4 | 0 | 1 | 0 |
| 6 | 3 | *17 | 0 | *13 | 7 | 3 | #13 | 2 | #12 | 1 | 10 | ‡16 | ‡15 | 3 | 2 | 4 | 2 | 0 | 0 |
| 7 | 6 | *12 | 2 | 9 | 7 | 3 | #14 | 3 | #12 | 0 | †16 | ‡18 | ‡13 | 2 | 1 | 6 | 0 | 1 | 1 |
| 8 | 2 | *6 | 3 | 3 | 2 | 2 | #6 | 0 | #6 | 2 | 2 | ‡9 | ‡6 | 1 | 0 | 3 | 0 | 1 | 1 |
| 9 | 2 | *11 | 1 | *9 | 3 | 2 | #11 | 1 | #10 | 1 | 1 | ‡12 | 7 | 0 | 1 | 5 | 0 | 0 | 0 |
The counts listed are subsets of the numbers in the column “Phenotypes with limit cycles” in Table 1. Parameters that are present in all phenotypes, due to the model design, are not shown (vs, vx, KA). The generic K parameter modulates the strength of the unique new inhibitions in designs 4–9. For example, in Design 4, K represents the parameter Kzx, which refers to the transcriptional inhibition of Clb2/Cdk1 (z) on Clb5/Cdk1 (x). Parameters that are part of terms that were dominant in more than 60% of all phenotypes that yielded limit cycles per design (Table 1) are marked with symbols in groups: activatory (*) and inhibitory (#) interactions among the Clb/Cdk1 complexes, new inhibitory interactions in designs 4–9 (†), and basal synthesis and degradation reactions (‡).