|
|
|
|
|
Internal Validations
|
We excluded the protein-protein interactions which are reported only in high-throughput experiments and generated 24 network models. Table S1 summarizes the internal validations on these restricted network models; overall, 17 out of 24 models contain pathways which are at least partially corroborated from previous studies or genes enriched with specific functional categories.
Table S1: Internal
validation for 17 out of 24 restricted network models.
|
Model
|
# Genes
|
Validated literature pathway
|
Refs.
|
Enriched MIPS Function
|
|
0
|
109
|
Kss1/Fus3-Ste12
(mating response and filamentous growth)
|
Elion et al. 1993
|
cell fate (1.48x10-7);
metabolism (0.0067)
|
|
1
|
69
|
Sok2-Msn4
(PKA pathway)
|
Smith et al. 1998
|
|
|
2
|
44
|
Tup1/Ssn6-Nrg1
(glucose metabolism)
|
Park et al. 1999
|
transport (1.05x10-5);
metabolism (5.41x10-4)
|
|
3
|
58
|
Tup1/Ssn6-α2/Mcm1
(mating response)
|
Wahi et al. 1995
|
cell fate (1.12x10-5)
|
|
4
|
44
|
Swi4-Ndd1-Ace2
(cell cycle)
|
Lew et al. 2001
|
|
|
6
|
36
|
Slt2-Rlm1/Swi4
(PKC pathway)
|
Jung et al. 1999
|
|
|
7
|
13
|
Cmd1-Cna1-Skn7
(calcium signaling)
|
Williams et al. 2001
|
|
|
8
|
9
|
|
|
cell defense (6.33x10-6)
|
|
10
|
12
|
Med2-Gal11-Gal4
(general transcription)
|
Park et al. 2000
|
|
|
12
|
7
|
|
|
metabolism (0.026)
|
|
13
|
17
|
|
|
metabolism (1.49x10-5)
|
|
14
|
6
|
Gcn4-Met4
(methionine synthesis)
|
|
metabolism (2.88x10-4)
|
|
16
|
9
|
Ste12-Mcm1
(mating response)
|
|
cell fate (4.55x10-8);
homeostasis (0.0012);
cell communication (0.0345)
|
|
17
|
13
|
Cka2-Abf1
(casein kinase pathway)
|
|
|
|
20
|
5
|
|
|
metabolism (0.0017)
|
|
22
|
8
|
Cka2-Abf1
(casein kinase pathway)
|
|
|
|
25
|
7
|
Cka2-Abf1
(casein kinase pathway)
|
|
|
|
|
|
|
|
|
|
|
