Table 1

Internal validation for 21 of the 38 inferred models

Model

Number of genes

Number of variants

Validated literature pathway

Enriched MIPS functions


0

130

1

Kss1/Fus3-Ste12 (mating response and filamentous growth)

Cell fate (1.48 × 10-7); metabolism (0.0067)

1

69

8

Sok2-Msn4 (PKA pathway)

2

63

16

Tup1-Hhf1 (histone regulation)

Protein synthesis (7.13 × 10-8)

3

44

2

Tup1/Ssn6-Nrg1 (glucose metabolism)

Transport (1.05 x 10.5); metabolism (5.41 × 10-4)

4

58

8

Tup1/Ssn6-α2/Mcm1 (mating response)

Cell fate (1.12 × 10-5);

5

58

4

Rpd3-Abf1 (histone modification)

6

44

2

Swi4-Ndd1-Ace2 (cell cycle)

7

26

4

Cell cycle (0.035)

8

36

8

Slt2-Rlm1/Swi4 (PKC pathway)

10

45

16

Med2-Gal4/Gcn4 (general transcription)

15

13

4

Cmd1-Cna1-Skn7 (calcium signaling)

19

9

4

Cell defense (6.33 × 10-6)

23

17

2

Metabolism (1.49 × 10-6);energy (0.04)

26

8

8

Cell defense (9.62 × 10-5)

29

9

4

Yap1-Cad1 (metal response)

30

12

4

Med2-Srb6-Gal4 (general transcription)

32

12

4

Med2-Gal11-Gal4 (general transcription)

33

12

4

Med2-Srb5-Gal4 (general transcription)

34

9

4

Ste12-Mcm1 (mating response)

Cell fate (4.55 × 10-8); homeostasis (0.0012); cell communication (0.0345)

36

7

4

Metabolism (0.0258)

40

5

2

Metabolism (0.0017)


The number of genes and variants are shown for each model along with the results of our preliminary validations. Each variant corresponds to a distinct set of functional annotations on the interactions in the model (directions and regulatory effects, see text). For Model 0, the expression data implied a unique set of annotations; for all other models multiple sets of annotations were possible. Each model was validated if its pathways were (wholly or partially) cited in previous studies or its downstream genes were significantly enriched for MIPS functional categories (p ≤ 0.05; hypergeometric test with Bonferroni correction).

Yeang et al. Genome Biology 2005 6:R62   doi:10.1186/gb-2005-6-7-r62

Open Data