Modeling Dependencies in Protein-DNA Binding Sites:
Analysis of Yeast Clusters

Another rich collection of gene clusters, based upon functional annotations were collected by Hughes et al, 2000. In the analysis of this data, we've considered only the experiments were at least 50 target genes had a significant p-value of 0.01. For each of those 43 clusters, we've performed a 5-fold cross validation test, learning a model on 80% of the sites, and predicting if there will be a binding within the other 20%. We've repaeted this procedure for all our various models (PSSM, Tree, Mixture of PSSMs & Mixture of Trees), and calculated the Sensitivity and Specificity measures, as well as the hypergeometric p-value of this partition. In the following table we present these results, as well as additional raw information.

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

1

aminoacid_biosynthesis
(ROC)
114 regulated

16%, 31%
1.3e-16
(pic) (net)

16%, 30%
1.9e-16
(pic) (net)

17%, 35%
1.3e-18
(pic) (net)
Clust=( 0.29 0.71 )

5%, 10%
3.6e-03
(pic) (net)
Clust=( 0.34 0.66 )

2

aminoacid_metabolism
(ROC)
173 regulated

13%, 34%
6.0e-17
(pic) (net)

13%, 34%
6.0e-17
(pic) (net)

10%, 30%
3.4e-12
(pic) (net)
Clust=( 0.59 0.41 )

4%, 12%
4.3e-03
(pic) (net)
Clust=( 0.54 0.46 )

3

assembly_of_protein_complexes
(ROC)
85 regulated

3%, 5%
8.5e-02
(pic) (net)

3%, 5%
9.3e-02
(pic) (net)

2%, 2%
4.5e-01
(pic) (net)
Clust=( 0.34 0.66 )

1%, 1%
6.5e-01
(pic) (net)
Clust=( 0.54 0.46 )

4

biogenesis_of_cell_wall
(ROC)
94 regulated

3%, 5%
9.9e-02
(pic) (net)

3%, 5%
9.9e-02
(pic) (net)

2%, 3%
3.8e-01
(pic) (net)
Clust=( 0.49 0.51 )

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.38 0.62 )

5

budding_cell_polarity_and_filament_formation
(ROC)
159 regulated

0%, 1%
9.5e-01
(pic) (net)

0%, 1%
9.5e-01
(pic) (net)

3%, 3%
6.3e-01
(pic) (net)
Clust=( 0.37 0.63 )

1%, 2%
8.6e-01
(pic) (net)
Clust=( 0.66 0.34 )

6

carbohydrate_utilization
(ROC)
249 regulated

4%, 13%
7.2e-03
(pic) (net)

4%, 13%
6.5e-03
(pic) (net)

3%, 10%
4.8e-02
(pic) (net)
Clust=( 0.40 0.60 )

2%, 7%
2.1e-01
(pic) (net)
Clust=( 0.50 0.50 )

7

cell_cycle_control_and_mitosis
(ROC)
289 regulated

2%, 11%
1.0e-01
(pic) (net)

2%, 10%
1.7e-01
(pic) (net)

4%, 8%
1.5e-01
(pic) (net)
Clust=( 0.63 0.37 )

3%, 8%
2.5e-01
(pic) (net)
Clust=( 0.76 0.24 )

8

cell_growth
(ROC)
68 regulated

1%, 2%
4.7e-01
(pic) (net)

1%, 2%
4.5e-01
(pic) (net)

1%, 1%
6.3e-01
(pic) (net)
Clust=( 0.55 0.45 )

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.75 0.25 )

9

cellular_import
(ROC)
95 regulated

3%, 5%
1.3e-01
(pic) (net)

3%, 5%
9.7e-02
(pic) (net)

4%, 4%
1.0e-01
(pic) (net)
Clust=( 0.34 0.66 )

7%, 10%
3.9e-04
(pic) (net)
Clust=( 0.43 0.57 )

10

cytoplasmic_degradation
(ROC)
93 regulated

33%, 28%
1.0e-28
(pic) (net)

31%, 28%
1.5e-26
(pic) (net)

20%, 20%
1.6e-14
(pic) (net)
Clust=( 0.60 0.40 )

13%, 21%
1.6e-10
(pic) (net)
Clust=( 0.68 0.32 )

11

detoxificaton
(ROC)
85 regulated

5%, 7%
7.4e-03
(pic) (net)

7%, 9%
1.4e-03
(pic) (net)

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.48 0.52 )

1%, 1%
6.4e-01
(pic) (net)
Clust=( 0.36 0.64 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

12

dna_synthesis_and_replication
(ROC)
80 regulated

12%, 17%
4.0e-08
(pic) (net)

12%, 17%
3.4e-08
(pic) (net)

10%, 11%
3.1e-05
(pic) (net)
Clust=( 0.61 0.39 )

5%, 6%
2.9e-02
(pic) (net)
Clust=( 0.50 0.50 )

13

glucose_metabolism
(ROC)
191 regulated

3%, 11%
1.3e-02
(pic) (net)

3%, 11%
1.7e-02
(pic) (net)

4%, 9%
2.1e-02
(pic) (net)
Clust=( 0.37 0.63 )

1%, 3%
7.1e-01
(pic) (net)
Clust=( 0.50 0.50 )

14

homeostasis_of_other_ions
(ROC)
58 regulated

3%, 3%
1.6e-01
(pic) (net)

3%, 3%
1.4e-01
(pic) (net)

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.55 0.45 )

3%, 3%
1.4e-01
(pic) (net)
Clust=( 0.48 0.52 )

15

lipid_fattyacid_and_sterol_biosynthesis
(ROC)
91 regulated

5%, 7%
1.0e-02
(pic) (net)

4%, 6%
4.0e-02
(pic) (net)

2%, 3%
3.4e-01
(pic) (net)
Clust=( 0.37 0.63 )

1%, 2%
5.9e-01
(pic) (net)
Clust=( 0.46 0.54 )

16

meiosis
(ROC)
91 regulated

18%, 13%
1.9e-10
(pic) (net)

18%, 14%
9.9e-11
(pic) (net)

10%, 9%
3.0e-05
(pic) (net)
Clust=( 0.40 0.60 )

3%, 3%
2.0e-01
(pic) (net)
Clust=( 0.56 0.44 )

17

metabolism_of_vitamins_cofactors_and_prosthetic_groups
(ROC)
59 regulated

3%, 3%
1.8e-01
(pic) (net)

3%, 3%
1.8e-01
(pic) (net)

3%, 2%
2.4e-01
(pic) (net)
Clust=( 0.38 0.62 )

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.51 0.49 )

18

mitochondrial_organization
(ROC)
320 regulated

6%, 36%
8.9e-11
(pic) (net)

6%, 35%
1.9e-10
(pic) (net)

5%, 27%
2.0e-06
(pic) (net)
Clust=( 0.45 0.55 )

1%, 8%
3.7e-01
(pic) (net)
Clust=( 0.35 0.65 )

19

mitochondrial_transport
(ROC)
72 regulated

4%, 6%
4.1e-02
(pic) (net)

5%, 8%
6.5e-03
(pic) (net)

4%, 4%
9.8e-02
(pic) (net)
Clust=( 0.40 0.60 )

1%, 1%
6.1e-01
(pic) (net)
Clust=( 0.56 0.44 )

20

nuclear_organization
(ROC)
670 regulated

3%, 38%
5.0e-06
(pic) (net)

3%, 39%
2.6e-06
(pic) (net)

3%, 18%
1.5e-01
(pic) (net)
Clust=( 0.75 0.25 )

3%, 15%
4.6e-01
(pic) (net)
Clust=( 0.17 0.83 )

21

organization_of_cytoplasm
(ROC)
531 regulated

11%, 51%
1.3e-26
(pic) (net)

11%, 52%
2.8e-27
(pic) (net)

17%, 28%
4.8e-18
(pic) (net)
Clust=( 0.37 0.63 )

15%, 21%
5.3e-09
(pic) (net)
Clust=( 0.62 0.38 )

22

organization_of_cytoskeleton
(ROC)
95 regulated

4%, 9%
1.3e-02
(pic) (net)

3%, 5%
9.3e-02
(pic) (net)

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.41 0.59 )

2%, 2%
4.4e-01
(pic) (net)
Clust=( 0.38 0.62 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

23

organization_of_endoplasmatic_reticulum
(ROC)
108 regulated

1%, 4%
3.0e-01
(pic) (net)

1%, 4%
2.7e-01
(pic) (net)

2%, 4%
2.3e-01
(pic) (net)
Clust=( 0.39 0.61 )

0%, 1%
7.7e-01
(pic) (net)
Clust=( 0.32 0.68 )

24

organization_of_golgi
(ROC)
56 regulated

3%, 4%
1.2e-01
(pic) (net)

3%, 4%
1.2e-01
(pic) (net)

10%, 7%
3.5e-04
(pic) (net)
Clust=( 0.49 0.51 )

3%, 3%
1.9e-01
(pic) (net)
Clust=( 0.31 0.69 )

25

organization_of_plasma_membrane
(ROC)
128 regulated

0%, 2%
7.7e-01
(pic) (net)

0%, 2%
7.6e-01
(pic) (net)

1%, 1%
9.6e-01
(pic) (net)
Clust=( 0.79 0.21 )

3%, 4%
2.6e-01
(pic) (net)
Clust=( 0.60 0.40 )

26

other_transcription_activities
(ROC)
57 regulated

7%, 4%
2.0e-02
(pic) (net)

5%, 3%
7.6e-02
(pic) (net)

7%, 6%
8.0e-03
(pic) (net)
Clust=( 0.50 0.50 )

3%, 2%
2.2e-01
(pic) (net)
Clust=( 0.49 0.51 )

27

other_transport_facilitators
(ROC)
54 regulated

11%, 4%
4.2e-03
(pic) (net)

9%, 4%
1.5e-02
(pic) (net)

3%, 2%
2.1e-01
(pic) (net)
Clust=( 0.32 0.68 )

3%, 3%
1.5e-01
(pic) (net)
Clust=( 0.58 0.42 )

28

pheromone_response_matingtype_determination_sexspecific_proteins
(ROC)
150 regulated

2%, 9%
5.4e-02
(pic) (net)

2%, 9%
5.4e-02
(pic) (net)

4%, 5%
1.3e-01
(pic) (net)
Clust=( 0.25 0.75 )

1%, 3%
6.0e-01
(pic) (net)
Clust=( 0.36 0.64 )

29

proteases
(ROC)
67 regulated

2%, 4%
1.5e-01
(pic) (net)

2%, 4%
1.4e-01
(pic) (net)

1%, 1%
7.1e-01
(pic) (net)
Clust=( 0.25 0.75 )

1%, 1%
6.7e-01
(pic) (net)
Clust=( 0.69 0.31 )

30

protein_kinase
(ROC)
128 regulated

1%, 2%
5.8e-01
(pic) (net)

1%, 3%
5.7e-01
(pic) (net)

7%, 3%
3.8e-01
(pic) (net)
Clust=( 0.52 0.48 )

0%, 1%
8.9e-01
(pic) (net)
Clust=( 0.72 0.28 )

31

protein_targeting_sorting_and_translocation
(ROC)
110 regulated

2%, 7%
8.3e-02
(pic) (net)

2%, 6%
9.2e-02
(pic) (net)

1%, 3%
4.6e-01
(pic) (net)
Clust=( 0.40 0.60 )

1%, 3%
3.7e-01
(pic) (net)
Clust=( 0.32 0.68 )

32

recombination_and_dna_repair
(ROC)
83 regulated

3%, 5%
9.9e-02
(pic) (net)

3%, 4%
1.0e-01
(pic) (net)

1%, 1%
7.1e-01
(pic) (net)
Clust=( 0.69 0.31 )

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.44 0.56 )

33

regulation_of_carbohydrate_utilization
(ROC)
116 regulated

3%, 6%
6.5e-02
(pic) (net)

3%, 6%
7.5e-02
(pic) (net)

4%, 4%
1.7e-01
(pic) (net)
Clust=( 0.65 0.35 )

1%, 3%
4.2e-01
(pic) (net)
Clust=( 0.47 0.53 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

34

respiration
(ROC)
70 regulated

15%, 18%
1.1e-09
(pic) (net)

15%, 18%
7.6e-10
(pic) (net)

8%, 9%
3.6e-04
(pic) (net)
Clust=( 0.44 0.56 )

2%, 4%
1.7e-01
(pic) (net)
Clust=( 0.69 0.31 )

35

ribosomal_proteins
(ROC)
198 regulated

39%, 49%
4.5e-69
(pic) (net)

39%, 49%
4.5e-69
(pic) (net)

43%, 48%
2.2e-75
(pic) (net)
Clust=( 0.45 0.55 )

34%, 44%
3.9e-56
(pic) (net)
Clust=( 0.64 0.36 )

36

rpl
(ROC)
76 regulated

67%, 28%
8.6e-56
(pic) (net)

68%, 29%
1.2e-57
(pic) (net)

67%, 29%
1.6e-56
(pic) (net)
Clust=( 0.22 0.78 )

55%, 28%
2.4e-44
(pic) (net)
Clust=( 0.82 0.18 )

37

rps
(ROC)
56 regulated

57%, 20%
1.8e-33
(pic) (net)

57%, 20%
1.4e-33
(pic) (net)

50%, 17%
1.1e-26
(pic) (net)
Clust=( 0.34 0.66 )

41%, 18%
1.8e-22
(pic) (net)
Clust=( 0.79 0.21 )

38

sporulation_and_germination
(ROC)
92 regulated

0%, 0%
1.0e+00
(pic) (net)

0%, 0%
1.0e+00
(pic) (net)

2%, 2%
6.1e-01
(pic) (net)
Clust=( 0.28 0.72 )

1%, 1%
8.0e-01
(pic) (net)
Clust=( 0.38 0.62 )

39

stress_response
(ROC)
138 regulated

4%, 10%
7.0e-03
(pic) (net)

4%, 11%
5.9e-03
(pic) (net)

2%, 5%
2.6e-01
(pic) (net)
Clust=( 0.39 0.61 )

2%, 4%
2.9e-01
(pic) (net)
Clust=( 0.51 0.49 )

40

transcriptional_control
(ROC)
295 regulated

3%, 18%
4.7e-03
(pic) (net)

3%, 17%
5.3e-03
(pic) (net)

3%, 9%
1.8e-01
(pic) (net)
Clust=( 0.21 0.79 )

1%, 8%
3.9e-01
(pic) (net)
Clust=( 0.48 0.52 )

41

transcription_factors
(ROC)
226 regulated

3%, 12%
2.1e-02
(pic) (net)

3%, 12%
2.3e-02
(pic) (net)

3%, 7%
1.5e-01
(pic) (net)
Clust=( 0.22 0.78 )

3%, 14%
3.1e-03
(pic) (net)
Clust=( 0.57 0.43 )

42

translation_initiation_elongation_and_termination
(ROC)
62 regulated

4%, 3%
8.7e-02
(pic) (net)

4%, 4%
7.4e-02
(pic) (net)

3%, 1%
4.4e-01
(pic) (net)
Clust=( 0.36 0.64 )

8%, 6%
4.7e-03
(pic) (net)
Clust=( 0.63 0.37 )

43

vesicular_transport_golgi_network_etc
(ROC)
93 regulated

2%, 4%
2.3e-01
(pic) (net)

1%, 2%
6.0e-01
(pic) (net)

1%, 1%
7.9e-01
(pic) (net)
Clust=( 0.64 0.36 )

2%, 3%
3.2e-01
(pic) (net)
Clust=( 0.31 0.69 )

#	NAME	PSSM (sens,spec,pval)	Tree (sens,spec,pval)	Mixture of PSSMs (sens,spec,pval)	Mixture of Trees (sens,spec,pval)
1	aminoacid_biosynthesis (ROC) 114 regulated	16%, 31% 1.3e-16 (pic) (net)	16%, 30% 1.9e-16 (pic) (net)	17%, 35% 1.3e-18 (pic) (net) Clust=( 0.29 0.71 )	5%, 10% 3.6e-03 (pic) (net) Clust=( 0.34 0.66 )
2	aminoacid_metabolism (ROC) 173 regulated	13%, 34% 6.0e-17 (pic) (net)	13%, 34% 6.0e-17 (pic) (net)	10%, 30% 3.4e-12 (pic) (net) Clust=( 0.59 0.41 )	4%, 12% 4.3e-03 (pic) (net) Clust=( 0.54 0.46 )
3	assembly_of_protein_complexes (ROC) 85 regulated	3%, 5% 8.5e-02 (pic) (net)	3%, 5% 9.3e-02 (pic) (net)	2%, 2% 4.5e-01 (pic) (net) Clust=( 0.34 0.66 )	1%, 1% 6.5e-01 (pic) (net) Clust=( 0.54 0.46 )
4	biogenesis_of_cell_wall (ROC) 94 regulated	3%, 5% 9.9e-02 (pic) (net)	3%, 5% 9.9e-02 (pic) (net)	2%, 3% 3.8e-01 (pic) (net) Clust=( 0.49 0.51 )	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.38 0.62 )
5	budding_cell_polarity_and_filament_formation (ROC) 159 regulated	0%, 1% 9.5e-01 (pic) (net)	0%, 1% 9.5e-01 (pic) (net)	3%, 3% 6.3e-01 (pic) (net) Clust=( 0.37 0.63 )	1%, 2% 8.6e-01 (pic) (net) Clust=( 0.66 0.34 )
6	carbohydrate_utilization (ROC) 249 regulated	4%, 13% 7.2e-03 (pic) (net)	4%, 13% 6.5e-03 (pic) (net)	3%, 10% 4.8e-02 (pic) (net) Clust=( 0.40 0.60 )	2%, 7% 2.1e-01 (pic) (net) Clust=( 0.50 0.50 )
7	cell_cycle_control_and_mitosis (ROC) 289 regulated	2%, 11% 1.0e-01 (pic) (net)	2%, 10% 1.7e-01 (pic) (net)	4%, 8% 1.5e-01 (pic) (net) Clust=( 0.63 0.37 )	3%, 8% 2.5e-01 (pic) (net) Clust=( 0.76 0.24 )
8	cell_growth (ROC) 68 regulated	1%, 2% 4.7e-01 (pic) (net)	1%, 2% 4.5e-01 (pic) (net)	1%, 1% 6.3e-01 (pic) (net) Clust=( 0.55 0.45 )	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.75 0.25 )
9	cellular_import (ROC) 95 regulated	3%, 5% 1.3e-01 (pic) (net)	3%, 5% 9.7e-02 (pic) (net)	4%, 4% 1.0e-01 (pic) (net) Clust=( 0.34 0.66 )	7%, 10% 3.9e-04 (pic) (net) Clust=( 0.43 0.57 )
10	cytoplasmic_degradation (ROC) 93 regulated	33%, 28% 1.0e-28 (pic) (net)	31%, 28% 1.5e-26 (pic) (net)	20%, 20% 1.6e-14 (pic) (net) Clust=( 0.60 0.40 )	13%, 21% 1.6e-10 (pic) (net) Clust=( 0.68 0.32 )
11	detoxificaton (ROC) 85 regulated	5%, 7% 7.4e-03 (pic) (net)	7%, 9% 1.4e-03 (pic) (net)	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.48 0.52 )	1%, 1% 6.4e-01 (pic) (net) Clust=( 0.36 0.64 )
#	NAME	PSSM (sens,spec,pval)	Tree (sens,spec,pval)	Mixture of PSSMs (sens,spec,pval)	Mixture of Trees (sens,spec,pval)
12	dna_synthesis_and_replication (ROC) 80 regulated	12%, 17% 4.0e-08 (pic) (net)	12%, 17% 3.4e-08 (pic) (net)	10%, 11% 3.1e-05 (pic) (net) Clust=( 0.61 0.39 )	5%, 6% 2.9e-02 (pic) (net) Clust=( 0.50 0.50 )
13	glucose_metabolism (ROC) 191 regulated	3%, 11% 1.3e-02 (pic) (net)	3%, 11% 1.7e-02 (pic) (net)	4%, 9% 2.1e-02 (pic) (net) Clust=( 0.37 0.63 )	1%, 3% 7.1e-01 (pic) (net) Clust=( 0.50 0.50 )
14	homeostasis_of_other_ions (ROC) 58 regulated	3%, 3% 1.6e-01 (pic) (net)	3%, 3% 1.4e-01 (pic) (net)	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.55 0.45 )	3%, 3% 1.4e-01 (pic) (net) Clust=( 0.48 0.52 )
15	lipid_fattyacid_and_sterol_biosynthesis (ROC) 91 regulated	5%, 7% 1.0e-02 (pic) (net)	4%, 6% 4.0e-02 (pic) (net)	2%, 3% 3.4e-01 (pic) (net) Clust=( 0.37 0.63 )	1%, 2% 5.9e-01 (pic) (net) Clust=( 0.46 0.54 )
16	meiosis (ROC) 91 regulated	18%, 13% 1.9e-10 (pic) (net)	18%, 14% 9.9e-11 (pic) (net)	10%, 9% 3.0e-05 (pic) (net) Clust=( 0.40 0.60 )	3%, 3% 2.0e-01 (pic) (net) Clust=( 0.56 0.44 )
17	metabolism_of_vitamins_cofactors_and_prosthetic_groups (ROC) 59 regulated	3%, 3% 1.8e-01 (pic) (net)	3%, 3% 1.8e-01 (pic) (net)	3%, 2% 2.4e-01 (pic) (net) Clust=( 0.38 0.62 )	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.51 0.49 )
18	mitochondrial_organization (ROC) 320 regulated	6%, 36% 8.9e-11 (pic) (net)	6%, 35% 1.9e-10 (pic) (net)	5%, 27% 2.0e-06 (pic) (net) Clust=( 0.45 0.55 )	1%, 8% 3.7e-01 (pic) (net) Clust=( 0.35 0.65 )
19	mitochondrial_transport (ROC) 72 regulated	4%, 6% 4.1e-02 (pic) (net)	5%, 8% 6.5e-03 (pic) (net)	4%, 4% 9.8e-02 (pic) (net) Clust=( 0.40 0.60 )	1%, 1% 6.1e-01 (pic) (net) Clust=( 0.56 0.44 )
20	nuclear_organization (ROC) 670 regulated	3%, 38% 5.0e-06 (pic) (net)	3%, 39% 2.6e-06 (pic) (net)	3%, 18% 1.5e-01 (pic) (net) Clust=( 0.75 0.25 )	3%, 15% 4.6e-01 (pic) (net) Clust=( 0.17 0.83 )
21	organization_of_cytoplasm (ROC) 531 regulated	11%, 51% 1.3e-26 (pic) (net)	11%, 52% 2.8e-27 (pic) (net)	17%, 28% 4.8e-18 (pic) (net) Clust=( 0.37 0.63 )	15%, 21% 5.3e-09 (pic) (net) Clust=( 0.62 0.38 )
22	organization_of_cytoskeleton (ROC) 95 regulated	4%, 9% 1.3e-02 (pic) (net)	3%, 5% 9.3e-02 (pic) (net)	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.41 0.59 )	2%, 2% 4.4e-01 (pic) (net) Clust=( 0.38 0.62 )
#	NAME	PSSM (sens,spec,pval)	Tree (sens,spec,pval)	Mixture of PSSMs (sens,spec,pval)	Mixture of Trees (sens,spec,pval)
23	organization_of_endoplasmatic_reticulum (ROC) 108 regulated	1%, 4% 3.0e-01 (pic) (net)	1%, 4% 2.7e-01 (pic) (net)	2%, 4% 2.3e-01 (pic) (net) Clust=( 0.39 0.61 )	0%, 1% 7.7e-01 (pic) (net) Clust=( 0.32 0.68 )
24	organization_of_golgi (ROC) 56 regulated	3%, 4% 1.2e-01 (pic) (net)	3%, 4% 1.2e-01 (pic) (net)	10%, 7% 3.5e-04 (pic) (net) Clust=( 0.49 0.51 )	3%, 3% 1.9e-01 (pic) (net) Clust=( 0.31 0.69 )
25	organization_of_plasma_membrane (ROC) 128 regulated	0%, 2% 7.7e-01 (pic) (net)	0%, 2% 7.6e-01 (pic) (net)	1%, 1% 9.6e-01 (pic) (net) Clust=( 0.79 0.21 )	3%, 4% 2.6e-01 (pic) (net) Clust=( 0.60 0.40 )
26	other_transcription_activities (ROC) 57 regulated	7%, 4% 2.0e-02 (pic) (net)	5%, 3% 7.6e-02 (pic) (net)	7%, 6% 8.0e-03 (pic) (net) Clust=( 0.50 0.50 )	3%, 2% 2.2e-01 (pic) (net) Clust=( 0.49 0.51 )
27	other_transport_facilitators (ROC) 54 regulated	11%, 4% 4.2e-03 (pic) (net)	9%, 4% 1.5e-02 (pic) (net)	3%, 2% 2.1e-01 (pic) (net) Clust=( 0.32 0.68 )	3%, 3% 1.5e-01 (pic) (net) Clust=( 0.58 0.42 )
28	pheromone_response_matingtype_determination_sexspecific_proteins (ROC) 150 regulated	2%, 9% 5.4e-02 (pic) (net)	2%, 9% 5.4e-02 (pic) (net)	4%, 5% 1.3e-01 (pic) (net) Clust=( 0.25 0.75 )	1%, 3% 6.0e-01 (pic) (net) Clust=( 0.36 0.64 )
29	proteases (ROC) 67 regulated	2%, 4% 1.5e-01 (pic) (net)	2%, 4% 1.4e-01 (pic) (net)	1%, 1% 7.1e-01 (pic) (net) Clust=( 0.25 0.75 )	1%, 1% 6.7e-01 (pic) (net) Clust=( 0.69 0.31 )
30	protein_kinase (ROC) 128 regulated	1%, 2% 5.8e-01 (pic) (net)	1%, 3% 5.7e-01 (pic) (net)	7%, 3% 3.8e-01 (pic) (net) Clust=( 0.52 0.48 )	0%, 1% 8.9e-01 (pic) (net) Clust=( 0.72 0.28 )
31	protein_targeting_sorting_and_translocation (ROC) 110 regulated	2%, 7% 8.3e-02 (pic) (net)	2%, 6% 9.2e-02 (pic) (net)	1%, 3% 4.6e-01 (pic) (net) Clust=( 0.40 0.60 )	1%, 3% 3.7e-01 (pic) (net) Clust=( 0.32 0.68 )
32	recombination_and_dna_repair (ROC) 83 regulated	3%, 5% 9.9e-02 (pic) (net)	3%, 4% 1.0e-01 (pic) (net)	1%, 1% 7.1e-01 (pic) (net) Clust=( 0.69 0.31 )	0%, 0% 1.0e+00 (pic) (net) Clust=( 0.44 0.56 )
33	regulation_of_carbohydrate_utilization (ROC) 116 regulated	3%, 6% 6.5e-02 (pic) (net)	3%, 6% 7.5e-02 (pic) (net)	4%, 4% 1.7e-01 (pic) (net) Clust=( 0.65 0.35 )	1%, 3% 4.2e-01 (pic) (net) Clust=( 0.47 0.53 )
#	NAME	PSSM (sens,spec,pval)	Tree (sens,spec,pval)	Mixture of PSSMs (sens,spec,pval)	Mixture of Trees (sens,spec,pval)
34	respiration (ROC) 70 regulated	15%, 18% 1.1e-09 (pic) (net)	15%, 18% 7.6e-10 (pic) (net)	8%, 9% 3.6e-04 (pic) (net) Clust=( 0.44 0.56 )	2%, 4% 1.7e-01 (pic) (net) Clust=( 0.69 0.31 )
35	ribosomal_proteins (ROC) 198 regulated	39%, 49% 4.5e-69 (pic) (net)	39%, 49% 4.5e-69 (pic) (net)	43%, 48% 2.2e-75 (pic) (net) Clust=( 0.45 0.55 )	34%, 44% 3.9e-56 (pic) (net) Clust=( 0.64 0.36 )
36	rpl (ROC) 76 regulated	67%, 28% 8.6e-56 (pic) (net)	68%, 29% 1.2e-57 (pic) (net)	67%, 29% 1.6e-56 (pic) (net) Clust=( 0.22 0.78 )	55%, 28% 2.4e-44 (pic) (net) Clust=( 0.82 0.18 )
37	rps (ROC) 56 regulated	57%, 20% 1.8e-33 (pic) (net)	57%, 20% 1.4e-33 (pic) (net)	50%, 17% 1.1e-26 (pic) (net) Clust=( 0.34 0.66 )	41%, 18% 1.8e-22 (pic) (net) Clust=( 0.79 0.21 )
38	sporulation_and_germination (ROC) 92 regulated	0%, 0% 1.0e+00 (pic) (net)	0%, 0% 1.0e+00 (pic) (net)	2%, 2% 6.1e-01 (pic) (net) Clust=( 0.28 0.72 )	1%, 1% 8.0e-01 (pic) (net) Clust=( 0.38 0.62 )
39	stress_response (ROC) 138 regulated	4%, 10% 7.0e-03 (pic) (net)	4%, 11% 5.9e-03 (pic) (net)	2%, 5% 2.6e-01 (pic) (net) Clust=( 0.39 0.61 )	2%, 4% 2.9e-01 (pic) (net) Clust=( 0.51 0.49 )
40	transcriptional_control (ROC) 295 regulated	3%, 18% 4.7e-03 (pic) (net)	3%, 17% 5.3e-03 (pic) (net)	3%, 9% 1.8e-01 (pic) (net) Clust=( 0.21 0.79 )	1%, 8% 3.9e-01 (pic) (net) Clust=( 0.48 0.52 )
41	transcription_factors (ROC) 226 regulated	3%, 12% 2.1e-02 (pic) (net)	3%, 12% 2.3e-02 (pic) (net)	3%, 7% 1.5e-01 (pic) (net) Clust=( 0.22 0.78 )	3%, 14% 3.1e-03 (pic) (net) Clust=( 0.57 0.43 )
42	translation_initiation_elongation_and_termination (ROC) 62 regulated	4%, 3% 8.7e-02 (pic) (net)	4%, 4% 7.4e-02 (pic) (net)	3%, 1% 4.4e-01 (pic) (net) Clust=( 0.36 0.64 )	8%, 6% 4.7e-03 (pic) (net) Clust=( 0.63 0.37 )
43	vesicular_transport_golgi_network_etc (ROC) 93 regulated	2%, 4% 2.3e-01 (pic) (net)	1%, 2% 6.0e-01 (pic) (net)	1%, 1% 7.9e-01 (pic) (net) Clust=( 0.64 0.36 )	2%, 3% 3.2e-01 (pic) (net) Clust=( 0.31 0.69 )