Table 1.
Parameters in each model. Number of parameters in cooperativity and quenching model combinations. 3 scaling factor parameters for Dorsal, Twist, and Snail are included in all models. Column 1 contains the nomenclature and number of parameters (in parentheses) for all 15 cooperativity models. Columns 2–9 in Row 2 contain nomenclature and number of parameters (in parentheses) for 8 quenching models. Each cooperativity and quenching scheme is described in the materials and methods section. The parameters being fitted for continuous functions are clearly laid out in this section. The following example illustrates the parameters in binned cooperativity and quenching functions. Model C14Q5: Parameters 1–3 are scaling factors for Dorsal, Twist, and Snail respectively. Parameters 4–15 reflect cooperativity (separate parameters existing for each type of protein-protein interaction)– parameters 4–6 represent Dorsal-Dorsal cooperativity (at 1–60 bp, 61–120 bp, and 121+ bp between bound Dorsal proteins), likewise parameters 7–9 represent Twist-Twist cooperativity, parameters 10–12 represent Dorsal-Twist cooperativity, and parameters 13–15 represent Snail-Snail cooperativity. Paramters 16–23 reflect quenching – parameters 16–19 represent Snail quenching Dorsal (at 1–25 bp, 26–50 bp, 51–75 bp, and 76+ bp between bound proteins), likewise parameters 20–23 represent Snail quenching Twist.
| Quenching Model | ||||||||
|---|---|---|---|---|---|---|---|---|
| Cooperativity Model | Q1 – MSB (0) | Q2 – Linear (2) | Q3 – Logistic (2) | Q4 – Gaussian (2) | Q5 – Binned 4_25 (8) |
Q6 – Binned 4_35 (8) |
Q7 – Binned 4_45 (8) |
Q8 – Binned 10_10 (20) |
| C1 – Linear (4) | 7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C2 – Logistic (4) | 7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C3 – Gaussian (4) | 7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C4 – Binned 2_25 (4) |
7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C5 – Binned 2_50 (4) |
7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C6 – Binned 2_75 (4) |
7 | 9 | 9 | 9 | 15 | 15 | 15 | 27 |
| C7 – Binned 3_50 (6) |
9 | 11 | 11 | 11 | 17 | 17 | 17 | 29 |
| C8 – Binned 3_60 (6) |
9 | 11 | 11 | 11 | 17 | 17 | 17 | 29 |
| C9 – Binned 3_70 (6) |
9 | 11 | 11 | 11 | 17 | 17 | 17 | 29 |
| C10 – Protein Binned 2_25 (8) |
11 | 13 | 13 | 13 | 19 | 19 | 19 | 31 |
| C11 – Protein Binned 2_50 (8) |
11 | 13 | 13 | 13 | 19 | 19 | 19 | 31 |
| C12 – Protein Binned 2_75 (8) |
11 | 13 | 13 | 13 | 19 | 19 | 19 | 31 |
| C13 – Protein Binned 3_50 (12) |
15 | 17 | 17 | 17 | 23 | 23 | 23 | 35 |
| C14 – Protein Binned 3_60 (12) |
15 | 17 | 17 | 17 | 23 | 23 | 23 | 35 |
| C15 – Protein Binned 3_70 (12) |
15 | 17 | 17 | 17 | 23 | 23 | 23 | 35 |