Table 3 Three Best-Fitting Models for Each Gene* Rules are in the same format as in Table 2 (see Methods). In this case, the genes in rows are inputs to genes in columns. The three best combinations of rules are in consecutive rows for each input; i.e., the best fit rule combination is the first row of each input block with the fit score (E) in the first row of the last block in the table. * Models are in rows, e.g., the best-fitting model for SIC1 has the input CLB5 with the rule (1 3 3), MBP1 with rule (3 1 1), and CDC6 with rule (1 2 3) corresponding to the fit error E = 0.689.

SIC1

CLB5

CDC20

CLN3

SWI6

CLN1

CLN2

CLB6

SWI4

CDC28

MBP1

CDC6

---

2 2 3

3 2 1

1 1 3

---

2 2 3

2 1 3

1 3 3

3 2 1

1 2 3

---

2 2 3

2 1 3

1 3 3

3 2 1

1 2 3

1 3 3

---

1 3 3

1 3 3

---

1 1 3

1 3 3

---

1 1 3

3 2 1

3 3 1

---

3 3 2

3 2 1

1 3 3

2 3 1

---

3 3 1

2 3 1

---

3 1 1

1 3 3

3 1 2

---

3 3 1

2 2 3

3 3 2

1 2 3

---

3 2 1

2 1 3

1 1 3

3 1 3

---

3 3 1

1 1 3

1 3 1

3 2 1

---

3 1 2

1 3 1

3 1 1

---

1 2 1

3 1 2

2 3 1

1 3 1

3 2 1

---

1 2 3

3 1 1

3 3 1

---

1 2 3

1 2 3

1 1 2

3 1 1

3 2 1

---

1 3 3

1 2 3

3 1 1

1 2 3

3 1 1

---

1 3 3

1 3 3

3 1 2

1 1 3

3 1 1

3 1 3

1 3 3

---

1 1 3

1 1 3

3 2 1

3 1 3

1 3 3

---

1 1 3

1 1 3

3 1 3

1 3 3

---

1 1 3

1 2 3

1 1 3

1 1 3

---

1 1 3

1 3 3

3 1 3

1 2 3

1 1 3

1 1 3

1 1 3

---

1 1 3

1 3 3

3 3 1

1 1 3

1 1 3

---

1 2 3

1 3 3

---

3 2 1

1 1 3

2 3 3

---

3 3 2

---

3 2 1

1 2 3

3 1 3

---

---

3 1 2

---

3 1 1

3 3 1

2 1 3

3 3 1

---

3 1 1

2 3 1

1 2 3

3 3 1

---

3 2 1

3 3 1

2 3 2

1 1 3

3 3 1

2 2 3

---

1 2 3

1 2 3

1 1 3

3 2 3

---

1 3 3

1 2 3

1 3 1

3 2 3

3 2 3

---

1 2 3

2 2 3

2 1 3

3 2 3

---

0.689

0.881

0.703

0.792

0.620

0.943

0.877

0.714

0.782

0.510

0.624

0.764

0.643

0.875

0.702

0.768

0.599

0.930

0.837

0.706

0.768

0.508

0.624

0.758

0.631

0.852

0.695

0.746

0.596

0.916

0.835

0.705

0.763

0.498

0.622

0.720