Modeling Dependencies in Protein-DNA Binding Sites:
Analysis of Yeast location Data
To test whether dependencies can be found in biological data, and whether they can improve binding site profiling and identification, we used a dataset of genome-wide Chromatin Immunoprecipitation (ChIP) location measurements for 106 yeast transcription factors in 146 experiments by Lee et al, 2002. This assay measures the binding affinities of a target transcription factor to promoter regions in vivo, providing valuable information about the binding specificity of transcription factors. However, it is important to keep in mind that it does not pinpoint the exact binding location.

In the analysis of this data, we've considered only the experiments were at least 10 target genes had a significant p-value of 0.001, and 50 with less than 0.01. For each of those 109 experiments, 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 compare their success on the test data.

In the cases for which there was a known motif in the TRANSFAC database, we compare our PSSM to it, and report whether we've found the known motif or not.

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

1

ABF1_YPD
(ROC)
535 regulated

82%, 39%
3.7e-203
(pic) (net)

84%, 37%
2.2e-204
(pic) (net)

86%, 36%
3.6e-209
(pic) (net)
Clust=( 0.08 0.92 )

83%, 38%
4.6e-202
(pic) (net)
Clust=( 0.66 0.34 )

F$ABF1_01
Found

2

ACE2_Cu2
(ROC)
63 regulated

10%, 2%
1.9e-02
(pic) (net)

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

15%, 3%
2.6e-03
(pic) (net)
Clust=( 0.54 0.46 )

21%, 3%
3.6e-04
(pic) (net)
Clust=( 0.43 0.57 )

3

ACE2_YPD
(ROC)
113 regulated

31%, 7%
8.1e-14
(pic) (net)

36%, 7%
1.5e-15
(pic) (net)

47%, 13%
5.6e-29
(pic) (net)
Clust=( 0.74 0.26 )

68%, 20%
2.1e-53
(pic) (net)
Clust=( 0.43 0.57 )

4

ARG80_YPD
(ROC)
94 regulated

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

5%, 1%
1.6e-01
(pic) (net)

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.03 0.97 )

23%, 4%
8.7e-05
(pic) (net)
Clust=( 0.27 0.73 )

5

ARG81_YPD
(ROC)
60 regulated

18%, 3%
6.3e-04
(pic) (net)

18%, 3%
6.3e-04
(pic) (net)

22%, 4%
2.7e-05
(pic) (net)
Clust=( 0.48 0.52 )

45%, 9%
6.6e-13
(pic) (net)
Clust=( 0.57 0.43 )

6

ARO80_YPD
(ROC)
92 regulated

3%, 1%
4.2e-01
(pic) (net)

6%, 1%
1.0e-01
(pic) (net)

15%, 4%
2.9e-04
(pic) (net)
Clust=( 0.17 0.83 )

48%, 14%
2.3e-20
(pic) (net)
Clust=( 0.55 0.45 )

7

ASH1_14hr_Butanol
(ROC)
180 regulated

15%, 7%
1.1e-06
(pic) (net)

15%, 7%
1.3e-06
(pic) (net)

22%, 7%
1.4e-09
(pic) (net)
Clust=( 0.33 0.67 )

35%, 14%
4.3e-22
(pic) (net)
Clust=( 0.63 0.37 )

8

BAS1_YPD
(ROC)
99 regulated

27%, 17%
2.1e-14
(pic) (net)

27%, 15%
1.4e-13
(pic) (net)

13%, 7%
1.5e-05
(pic) (net)
Clust=( 0.42 0.58 )

36%, 16%
1.9e-18
(pic) (net)
Clust=( 0.53 0.47 )

9

CAD1_YPD
(ROC)
79 regulated

23%, 13%
2.2e-10
(pic) (net)

23%, 13%
1.9e-10
(pic) (net)

26%, 10%
1.1e-10
(pic) (net)
Clust=( 0.46 0.54 )

55%, 13%
9.1e-25
(pic) (net)
Clust=( 0.74 0.26 )

10

CBF1_YPD
(ROC)
127 regulated

75%, 18%
2.4e-44
(pic) (net)

75%, 19%
1.6e-44
(pic) (net)

75%, 20%
1.1e-45
(pic) (net)
Clust=( 0.25 0.75 )

80%, 18%
2.0e-47
(pic) (net)
Clust=( 0.21 0.79 )

F$CBF1_B
Found

11

CIN5_YPD
(ROC)
257 regulated

16%, 26%
2.4e-19
(pic) (net)

16%, 26%
2.4e-19
(pic) (net)

22%, 35%
4.4e-31
(pic) (net)
Clust=( 0.34 0.66 )

20%, 26%
3.7e-24
(pic) (net)
Clust=( 0.65 0.35 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

12

CUP9_Cu2
(ROC)
144 regulated

33%, 17%
1.7e-17
(pic) (net)

35%, 14%
3.1e-17
(pic) (net)

44%, 12%
1.9e-20
(pic) (net)
Clust=( 0.80 0.20 )

75%, 17%
1.2e-42
(pic) (net)
Clust=( 0.68 0.32 )

13

CUP9_YPD
(ROC)
75 regulated

14%, 2%
8.2e-03
(pic) (net)

14%, 2%
7.1e-03
(pic) (net)

14%, 2%
5.7e-03
(pic) (net)
Clust=( 0.55 0.45 )

33%, 7%
1.3e-08
(pic) (net)
Clust=( 0.57 0.43 )

14

DAL81_YPD
(ROC)
91 regulated

12%, 5%
4.0e-04
(pic) (net)

12%, 5%
2.3e-04
(pic) (net)

12%, 4%
6.2e-04
(pic) (net)
Clust=( 0.50 0.50 )

38%, 13%
7.0e-17
(pic) (net)
Clust=( 0.66 0.34 )

15

DAL82_YPD
(ROC)
82 regulated

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

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

23%, 2%
1.2e-03
(pic) (net)
Clust=( 0.29 0.71 )

30%, 3%
7.5e-05
(pic) (net)
Clust=( 0.51 0.49 )

16

DIG1_14hr_Butanol
(ROC)
166 regulated

9%, 15%
1.3e-07
(pic) (net)

9%, 15%
1.1e-07
(pic) (net)

6%, 10%
1.3e-04
(pic) (net)
Clust=( 0.31 0.69 )

18%, 29%
4.1e-20
(pic) (net)
Clust=( 0.30 0.70 )

17

DIG1_90min_Butanol
(ROC)
143 regulated

3%, 2%
1.4e-01
(pic) (net)

3%, 2%
1.4e-01
(pic) (net)

1%, 1%
5.0e-01
(pic) (net)
Clust=( 0.43 0.57 )

18%, 12%
5.7e-10
(pic) (net)
Clust=( 0.41 0.59 )

18

DIG1_Alpha
(ROC)
108 regulated

1%, 1%
5.3e-01
(pic) (net)

7%, 6%
2.0e-03
(pic) (net)

20%, 14%
2.4e-12
(pic) (net)
Clust=( 0.41 0.59 )

30%, 22%
5.4e-23
(pic) (net)
Clust=( 0.57 0.43 )

19

DIG1_YPD
(ROC)
84 regulated

8%, 6%
2.5e-03
(pic) (net)

11%, 7%
2.0e-04
(pic) (net)

17%, 7%
6.3e-06
(pic) (net)
Clust=( 0.23 0.77 )

34%, 10%
6.6e-13
(pic) (net)
Clust=( 0.54 0.46 )

20

FHL1_YPD
(ROC)
208 regulated

74%, 50%
1.4e-163
(pic) (net)

75%, 51%
6.3e-169
(pic) (net)

78%, 51%
4.9e-178
(pic) (net)
Clust=( 0.17 0.83 )

82%, 56%
9.5e-202
(pic) (net)
Clust=( 0.84 0.16 )

21

FKH1_YPD
(ROC)
203 regulated

31%, 13%
3.8e-18
(pic) (net)

33%, 14%
2.9e-19
(pic) (net)

38%, 15%
3.6e-23
(pic) (net)
Clust=( 0.26 0.74 )

44%, 16%
4.1e-28
(pic) (net)
Clust=( 0.24 0.76 )

22

FKH2_YPD
(ROC)
204 regulated

34%, 24%
4.5e-34
(pic) (net)

35%, 25%
9.1e-36
(pic) (net)

35%, 19%
6.8e-31
(pic) (net)
Clust=( 0.15 0.85 )

42%, 27%
3.4e-44
(pic) (net)
Clust=( 0.21 0.79 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

23

FZF1_YPD
(ROC)
97 regulated

23%, 3%
1.8e-04
(pic) (net)

23%, 4%
1.2e-04
(pic) (net)

35%, 1%
1.3e-04
(pic) (net)
Clust=( 0.03 0.97 )

35%, 3%
4.0e-06
(pic) (net)
Clust=( 0.68 0.32 )

24

GAL4_Cu2
(ROC)
76 regulated

42%, 15%
1.2e-18
(pic) (net)

37%, 11%
2.5e-14
(pic) (net)

51%, 16%
4.8e-23
(pic) (net)
Clust=( 0.55 0.45 )

68%, 17%
1.2e-32
(pic) (net)
Clust=( 0.47 0.53 )

F$GAL4_01
F$GAL4_C
Not Found

25

GAL4_Galactose
(ROC)
180 regulated

11%, 9%
2.3e-06
(pic) (net)

16%, 12%
1.7e-10
(pic) (net)

14%, 11%
5.2e-09
(pic) (net)
Clust=( 0.47 0.53 )

28%, 18%
1.6e-23
(pic) (net)
Clust=( 0.28 0.72 )

F$GAL4_01
F$GAL4_C
Not Found

26

GAL4_YPD
(ROC)
86 regulated

23%, 3%
2.7e-04
(pic) (net)

23%, 3%
1.8e-04
(pic) (net)

35%, 3%
2.7e-06
(pic) (net)
Clust=( 0.64 0.36 )

58%, 6%
2.3e-12
(pic) (net)
Clust=( 0.44 0.56 )

F$GAL4_01
F$GAL4_C
Not Found

27

GAT3_YPD
(ROC)
178 regulated

50%, 27%
1.9e-40
(pic) (net)

48%, 25%
9.8e-38
(pic) (net)

51%, 26%
2.5e-41
(pic) (net)
Clust=( 0.20 0.80 )

74%, 25%
2.6e-62
(pic) (net)
Clust=( 0.65 0.35 )

28

GCN4_3AT
(ROC)
330 regulated

27%, 45%
2.3e-39
(pic) (net)

28%, 49%
6.0e-42
(pic) (net)

27%, 35%
1.3e-34
(pic) (net)
Clust=( 0.81 0.19 )

32%, 31%
1.0e-39
(pic) (net)
Clust=( 0.23 0.77 )

F$GCN4_01
Found

29

GCN4_YPD
(ROC)
133 regulated

37%, 30%
6.1e-34
(pic) (net)

37%, 29%
1.2e-33
(pic) (net)

28%, 22%
2.0e-22
(pic) (net)
Clust=( 0.40 0.60 )

48%, 29%
1.7e-44
(pic) (net)
Clust=( 0.25 0.75 )

F$GCN4_01
Found

30

GCR2_YPD
(ROC)
98 regulated

6%, 2%
6.8e-02
(pic) (net)

9%, 3%
1.0e-02
(pic) (net)

12%, 3%
2.8e-03
(pic) (net)
Clust=( 0.03 0.97 )

31%, 10%
2.0e-11
(pic) (net)
Clust=( 0.46 0.54 )

31

GLN3_YPD
(ROC)
79 regulated

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

7%, 1%
1.5e-01
(pic) (net)

7%, 1%
1.3e-01
(pic) (net)
Clust=( 0.18 0.82 )

30%, 3%
7.8e-05
(pic) (net)
Clust=( 0.47 0.53 )

32

GRF10Pho2_Pi-
(ROC)
126 regulated

2%, 1%
3.5e-01
(pic) (net)

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

2%, 1%
3.8e-01
(pic) (net)
Clust=( 0.53 0.47 )

33%, 11%
1.4e-14
(pic) (net)
Clust=( 0.38 0.62 )

33

GRF10Pho2_YPD
(ROC)
108 regulated

4%, 1%
2.8e-01
(pic) (net)

4%, 1%
2.8e-01
(pic) (net)

8%, 2%
4.5e-02
(pic) (net)
Clust=( 0.19 0.81 )

30%, 7%
3.8e-08
(pic) (net)
Clust=( 0.70 0.30 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

34

GTS1_YPD
(ROC)
82 regulated

30%, 5%
1.1e-05
(pic) (net)

30%, 5%
1.4e-05
(pic) (net)

30%, 4%
3.7e-05
(pic) (net)
Clust=( 0.40 0.60 )

30%, 3%
8.9e-05
(pic) (net)
Clust=( 0.49 0.51 )

35

HAA1_Cu2
(ROC)
70 regulated

16%, 2%
3.1e-03
(pic) (net)

16%, 2%
3.9e-03
(pic) (net)

16%, 2%
4.4e-03
(pic) (net)
Clust=( 0.21 0.79 )

61%, 8%
9.8e-15
(pic) (net)
Clust=( 0.50 0.50 )

36

HAL9_YPD
(ROC)
54 regulated

25%, 4%
6.5e-05
(pic) (net)

25%, 5%
2.6e-05
(pic) (net)

31%, 3%
3.8e-05
(pic) (net)
Clust=( 0.59 0.41 )

43%, 8%
9.7e-10
(pic) (net)
Clust=( 0.50 0.50 )

37

HAP3_YPD
(ROC)
128 regulated

33%, 4%
4.7e-06
(pic) (net)

33%, 4%
5.4e-06
(pic) (net)

46%, 4%
2.2e-08
(pic) (net)
Clust=( 0.33 0.67 )

53%, 5%
8.5e-10
(pic) (net)
Clust=( 0.62 0.38 )

F$HAP234_01
Not Found

38

HAP4_YPD
(ROC)
127 regulated

28%, 18%
1.7e-18
(pic) (net)

34%, 23%
6.3e-25
(pic) (net)

29%, 18%
2.6e-19
(pic) (net)
Clust=( 0.51 0.49 )

51%, 25%
9.8e-40
(pic) (net)
Clust=( 0.65 0.35 )

F$HAP234_01
Found

39

HAP5_YPD
(ROC)
60 regulated

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

15%, 2%
1.4e-02
(pic) (net)

15%, 3%
5.6e-03
(pic) (net)
Clust=( 0.54 0.46 )

15%, 2%
1.6e-02
(pic) (net)
Clust=( 0.39 0.61 )

40

HIR1_YPD
(ROC)
87 regulated

14%, 4%
6.4e-04
(pic) (net)

17%, 7%
1.5e-05
(pic) (net)

25%, 6%
5.7e-07
(pic) (net)
Clust=( 0.22 0.78 )

53%, 16%
5.5e-21
(pic) (net)
Clust=( 0.53 0.47 )

41

HIR2_YPD
(ROC)
71 regulated

9%, 2%
2.4e-02
(pic) (net)

9%, 2%
2.4e-02
(pic) (net)

14%, 2%
4.7e-03
(pic) (net)
Clust=( 0.38 0.62 )

38%, 7%
1.2e-09
(pic) (net)
Clust=( 0.71 0.29 )

42

HMS1_YPD
(ROC)
57 regulated

40%, 5%
3.4e-06
(pic) (net)

40%, 5%
3.8e-06
(pic) (net)

40%, 4%
1.0e-05
(pic) (net)
Clust=( 0.64 0.36 )

50%, 5%
1.2e-07
(pic) (net)
Clust=( 0.33 0.67 )

43

HSF1_Heat
(ROC)
119 regulated

43%, 16%
4.0e-15
(pic) (net)

43%, 12%
1.2e-13
(pic) (net)

65%, 13%
9.8e-22
(pic) (net)
Clust=( 0.46 0.54 )

82%, 18%
2.1e-31
(pic) (net)
Clust=( 0.44 0.56 )

F$HSF_01
Found

44

HSF1_YPD
(ROC)
155 regulated

32%, 21%
2.8e-21
(pic) (net)

29%, 20%
2.5e-18
(pic) (net)

49%, 25%
1.3e-34
(pic) (net)
Clust=( 0.39 0.61 )

58%, 29%
1.1e-43
(pic) (net)
Clust=( 0.46 0.54 )

F$HSF_04/5
Found

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

45

IME4_YPD
(ROC)
64 regulated

61%, 6%
9.3e-19
(pic) (net)

58%, 5%
1.6e-17
(pic) (net)

69%, 5%
8.7e-20
(pic) (net)
Clust=( 0.40 0.60 )

72%, 7%
2.3e-25
(pic) (net)
Clust=( 0.64 0.36 )

46

INO4_YPD
(ROC)
152 regulated

77%, 21%
1.3e-25
(pic) (net)

77%, 21%
1.3e-25
(pic) (net)

50%, 9%
1.1e-12
(pic) (net)
Clust=( 0.55 0.45 )

16%, 2%
3.4e-03
(pic) (net)
Clust=( 0.41 0.59 )

47

IXR1_YPD
(ROC)
99 regulated

9%, 3%
7.1e-03
(pic) (net)

9%, 4%
6.4e-03
(pic) (net)

12%, 5%
7.1e-04
(pic) (net)
Clust=( 0.42 0.58 )

21%, 7%
3.2e-07
(pic) (net)
Clust=( 0.37 0.63 )

48

LEU3_YPD
(ROC)
60 regulated

36%, 8%
4.0e-10
(pic) (net)

31%, 9%
4.7e-09
(pic) (net)

31%, 7%
2.3e-08
(pic) (net)
Clust=( 0.35 0.65 )

27%, 6%
8.4e-07
(pic) (net)
Clust=( 0.50 0.50 )

F$LEU3_B
Found

49

MAC1_Cu2
(ROC)
119 regulated

43%, 30%
5.8e-36
(pic) (net)

43%, 26%
5.9e-34
(pic) (net)

54%, 16%
1.0e-35
(pic) (net)
Clust=( 0.71 0.29 )

71%, 19%
8.2e-53
(pic) (net)
Clust=( 0.70 0.30 )

50

MAC1_YPD
(ROC)
111 regulated

21%, 9%
9.3e-08
(pic) (net)

18%, 9%
8.5e-07
(pic) (net)

31%, 10%
2.8e-11
(pic) (net)
Clust=( 0.51 0.49 )

56%, 16%
4.4e-24
(pic) (net)
Clust=( 0.45 0.55 )

51

MBP1_YPD
(ROC)
198 regulated

19%, 25%
1.5e-19
(pic) (net)

19%, 25%
1.5e-19
(pic) (net)

27%, 21%
5.9e-25
(pic) (net)
Clust=( 0.45 0.55 )

38%, 24%
2.7e-38
(pic) (net)
Clust=( 0.48 0.52 )

52

MCM1_Alpha
(ROC)
163 regulated

50%, 30%
6.6e-58
(pic) (net)

50%, 30%
4.7e-58
(pic) (net)

57%, 30%
3.8e-68
(pic) (net)
Clust=( 0.22 0.78 )

48%, 34%
1.3e-59
(pic) (net)
Clust=( 0.54 0.46 )

F$MCM1_01
Found

53

MCM1_YPD
(ROC)
191 regulated

51%, 31%
1.3e-53
(pic) (net)

49%, 30%
3.4e-50
(pic) (net)

49%, 26%
6.4e-47
(pic) (net)
Clust=( 0.09 0.91 )

58%, 30%
2.1e-60
(pic) (net)
Clust=( 0.53 0.47 )

F$MCM1_01
Found

54

MET31_YPD
(ROC)
82 regulated

20%, 5%
1.6e-05
(pic) (net)

20%, 5%
7.0e-06
(pic) (net)

10%, 4%
3.9e-03
(pic) (net)
Clust=( 0.65 0.35 )

37%, 10%
4.0e-13
(pic) (net)
Clust=( 0.73 0.27 )

55

MET4_YPD
(ROC)
89 regulated

50%, 14%
7.8e-18
(pic) (net)

50%, 14%
6.7e-18
(pic) (net)

26%, 8%
3.6e-08
(pic) (net)
Clust=( 0.57 0.43 )

53%, 11%
3.3e-18
(pic) (net)
Clust=( 0.42 0.58 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

56

MIG1_YPD
(ROC)
61 regulated

30%, 4%
1.8e-04
(pic) (net)

30%, 4%
1.5e-04
(pic) (net)

40%, 5%
3.6e-06
(pic) (net)
Clust=( 0.44 0.56 )

50%, 5%
1.8e-07
(pic) (net)
Clust=( 0.64 0.36 )

F$MIG1_01
Not Found

57

MOT3_YPD
(ROC)
63 regulated

9%, 1%
1.1e-01
(pic) (net)

18%, 3%
4.2e-03
(pic) (net)

18%, 2%
8.4e-03
(pic) (net)
Clust=( 0.23 0.77 )

27%, 3%
5.7e-04
(pic) (net)
Clust=( 0.47 0.53 )

58

MSN2_Acid
(ROC)
186 regulated

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

3%, 2%
1.5e-01
(pic) (net)

14%, 8%
7.8e-07
(pic) (net)
Clust=( 0.55 0.45 )

21%, 13%
8.4e-12
(pic) (net)
Clust=( 0.41 0.59 )

F$STRE_B
Not Found

59

MSN2_H2O2
(ROC)
162 regulated

12%, 8%
3.4e-06
(pic) (net)

21%, 16%
9.5e-14
(pic) (net)

17%, 9%
4.0e-08
(pic) (net)
Clust=( 0.36 0.64 )

39%, 20%
6.9e-27
(pic) (net)
Clust=( 0.47 0.53 )

F$STRE_B
Not Found

60

MSN4_Acid
(ROC)
98 regulated

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

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

10%, 1%
5.2e-02
(pic) (net)
Clust=( 0.40 0.60 )

42%, 5%
3.1e-09
(pic) (net)
Clust=( 0.74 0.26 )

61

MSN4_H2O2
(ROC)
175 regulated

9%, 5%
1.0e-03
(pic) (net)

9%, 5%
9.5e-04
(pic) (net)

11%, 5%
2.8e-04
(pic) (net)
Clust=( 0.46 0.54 )

11%, 5%
3.3e-04
(pic) (net)
Clust=( 0.62 0.38 )

62

MSN4_YPD
(ROC)
98 regulated

31%, 10%
3.9e-11
(pic) (net)

31%, 9%
7.0e-11
(pic) (net)

37%, 13%
5.0e-15
(pic) (net)
Clust=( 0.82 0.18 )

46%, 11%
2.2e-17
(pic) (net)
Clust=( 0.63 0.37 )

63

MSS11_14hr_Butanol
(ROC)
80 regulated

15%, 3%
6.6e-04
(pic) (net)

12%, 3%
3.4e-03
(pic) (net)

37%, 8%
3.1e-12
(pic) (net)
Clust=( 0.38 0.62 )

40%, 13%
5.7e-16
(pic) (net)
Clust=( 0.58 0.42 )

64

MSS11_YPD
(ROC)
133 regulated

4%, 1%
2.2e-01
(pic) (net)

14%, 4%
1.9e-03
(pic) (net)

23%, 5%
1.5e-05
(pic) (net)
Clust=( 0.71 0.29 )

61%, 11%
3.9e-18
(pic) (net)
Clust=( 0.45 0.55 )

65

MTH1_YPD
(ROC)
163 regulated

13%, 1%
4.5e-02
(pic) (net)

20%, 2%
3.3e-03
(pic) (net)

33%, 3%
3.4e-05
(pic) (net)
Clust=( 0.45 0.55 )

73%, 6%
9.2e-15
(pic) (net)
Clust=( 0.67 0.33 )

66

NDD1_YPD
(ROC)
159 regulated

28%, 14%
1.0e-19
(pic) (net)

23%, 13%
8.7e-16
(pic) (net)

27%, 13%
2.9e-18
(pic) (net)
Clust=( 0.28 0.72 )

40%, 23%
1.4e-37
(pic) (net)
Clust=( 0.58 0.42 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

67

NRG1_YPD
(ROC)
147 regulated

13%, 7%
3.6e-06
(pic) (net)

13%, 7%
2.7e-06
(pic) (net)

24%, 6%
1.5e-09
(pic) (net)
Clust=( 0.64 0.36 )

41%, 16%
7.0e-30
(pic) (net)
Clust=( 0.37 0.63 )

68

PDR1_YPD
(ROC)
145 regulated

23%, 21%
1.7e-16
(pic) (net)

23%, 17%
4.0e-15
(pic) (net)

32%, 12%
6.4e-18
(pic) (net)
Clust=( 0.82 0.18 )

52%, 16%
6.9e-34
(pic) (net)
Clust=( 0.36 0.64 )

69

PHD1_14hr_Butanol
(ROC)
230 regulated

6%, 8%
1.1e-03
(pic) (net)

5%, 7%
3.4e-03
(pic) (net)

7%, 9%
9.1e-05
(pic) (net)
Clust=( 0.43 0.57 )

22%, 23%
6.7e-25
(pic) (net)
Clust=( 0.50 0.50 )

70

PHD1_90min_Butanol
(ROC)
181 regulated

16%, 20%
3.1e-15
(pic) (net)

18%, 20%
7.5e-17
(pic) (net)

20%, 17%
9.8e-17
(pic) (net)
Clust=( 0.30 0.70 )

27%, 21%
9.2e-26
(pic) (net)
Clust=( 0.55 0.45 )

71

PHD1_YPD
(ROC)
178 regulated

6%, 7%
1.2e-03
(pic) (net)

8%, 9%
3.1e-05
(pic) (net)

12%, 9%
9.6e-07
(pic) (net)
Clust=( 0.25 0.75 )

17%, 14%
4.7e-12
(pic) (net)
Clust=( 0.59 0.41 )

72

PHO4_Pi-
(ROC)
157 regulated

21%, 18%
1.0e-15
(pic) (net)

21%, 18%
8.5e-16
(pic) (net)

21%, 18%
1.0e-15
(pic) (net)
Clust=( 0.48 0.52 )

35%, 20%
1.6e-27
(pic) (net)
Clust=( 0.44 0.56 )

F$PHO4_01
Found

73

PHO4_YPD
(ROC)
137 regulated

3%, 2%
2.0e-01
(pic) (net)

6%, 4%
1.1e-02
(pic) (net)

1%, 0%
7.0e-01
(pic) (net)
Clust=( 0.57 0.43 )

35%, 17%
1.3e-22
(pic) (net)
Clust=( 0.64 0.36 )

F$PHO4_01
Not Found

74

RCS1_YPD
(ROC)
91 regulated

12%, 6%
1.9e-04
(pic) (net)

9%, 3%
6.5e-03
(pic) (net)

16%, 6%
3.5e-05
(pic) (net)
Clust=( 0.13 0.87 )

32%, 9%
3.3e-11
(pic) (net)
Clust=( 0.43 0.57 )

75

RFX1_YPD
(ROC)
88 regulated

43%, 17%
7.7e-19
(pic) (net)

43%, 17%
6.4e-19
(pic) (net)

43%, 14%
1.5e-17
(pic) (net)
Clust=( 0.47 0.53 )

53%, 19%
3.9e-24
(pic) (net)
Clust=( 0.45 0.55 )

76

RGM1_YPD
(ROC)
126 regulated

34%, 3%
2.8e-07
(pic) (net)

46%, 5%
5.9e-11
(pic) (net)

50%, 4%
2.5e-11
(pic) (net)
Clust=( 0.46 0.54 )

73%, 7%
1.4e-21
(pic) (net)
Clust=( 0.34 0.66 )

77

RGT1_Low_Glucose
(ROC)
64 regulated

47%, 15%
3.5e-15
(pic) (net)

42%, 12%
7.0e-13
(pic) (net)

42%, 12%
7.0e-13
(pic) (net)
Clust=( 0.31 0.69 )

71%, 16%
8.7e-24
(pic) (net)
Clust=( 0.61 0.39 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

78

RLM1_14hr_Butanol
(ROC)
113 regulated

9%, 4%
6.9e-03
(pic) (net)

9%, 3%
7.8e-03
(pic) (net)

12%, 5%
4.5e-04
(pic) (net)
Clust=( 0.22 0.78 )

21%, 7%
7.8e-07
(pic) (net)
Clust=( 0.37 0.63 )

79

RLM1_YPD
(ROC)
96 regulated

2%, 1%
4.1e-01
(pic) (net)

2%, 1%
3.9e-01
(pic) (net)

2%, 0%
5.8e-01
(pic) (net)
Clust=( 0.38 0.62 )

13%, 6%
1.1e-04
(pic) (net)
Clust=( 0.32 0.68 )

80

RME1_YPD
(ROC)
62 regulated

6%, 1%
1.5e-01
(pic) (net)

6%, 1%
1.5e-01
(pic) (net)

20%, 3%
1.1e-03
(pic) (net)
Clust=( 0.31 0.69 )

33%, 5%
2.3e-06
(pic) (net)
Clust=( 0.36 0.64 )

81

RTG1_YPD
(ROC)
92 regulated

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

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

0%, 0%
1.0e+00
(pic) (net)
Clust=( 0.40 0.60 )

60%, 5%
4.5e-09
(pic) (net)
Clust=( 0.65 0.35 )

82

RTG3_Rapamycin
(ROC)
106 regulated

15%, 5%
8.3e-05
(pic) (net)

18%, 7%
2.7e-06
(pic) (net)

6%, 2%
8.0e-02
(pic) (net)
Clust=( 0.48 0.52 )

37%, 11%
4.8e-14
(pic) (net)
Clust=( 0.28 0.72 )

83

RTG3_YPD
(ROC)
88 regulated

12%, 2%
1.4e-02
(pic) (net)

12%, 3%
9.5e-03
(pic) (net)

18%, 4%
6.7e-04
(pic) (net)
Clust=( 0.69 0.31 )

12%, 2%
1.9e-02
(pic) (net)
Clust=( 0.78 0.22 )

84

SFP1_YPD
(ROC)
108 regulated

24%, 2%
9.9e-04
(pic) (net)

24%, 2%
7.9e-04
(pic) (net)

34%, 2%
2.9e-06
(pic) (net)
Clust=( 0.37 0.63 )

62%, 6%
4.2e-18
(pic) (net)
Clust=( 0.54 0.46 )

85

SKN7_YPD
(ROC)
198 regulated

20%, 17%
5.5e-17
(pic) (net)

19%, 16%
1.2e-14
(pic) (net)

24%, 18%
1.5e-20
(pic) (net)
Clust=( 0.46 0.54 )

35%, 20%
7.9e-31
(pic) (net)
Clust=( 0.37 0.63 )

86

SMP1_YPD
(ROC)
128 regulated

10%, 6%
1.2e-04
(pic) (net)

17%, 10%
9.9e-09
(pic) (net)

21%, 6%
1.5e-08
(pic) (net)
Clust=( 0.40 0.60 )

42%, 14%
7.7e-25
(pic) (net)
Clust=( 0.53 0.47 )

87

SOK2_14hr_Butanol
(ROC)
208 regulated

1%, 1%
6.8e-01
(pic) (net)

1%, 1%
6.9e-01
(pic) (net)

11%, 9%
2.9e-06
(pic) (net)
Clust=( 0.40 0.60 )

16%, 15%
8.1e-12
(pic) (net)
Clust=( 0.49 0.51 )

88

SOK2_YPD
(ROC)
100 regulated

5%, 1%
1.8e-01
(pic) (net)

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

5%, 1%
2.0e-01
(pic) (net)
Clust=( 0.34 0.66 )

29%, 4%
8.3e-06
(pic) (net)
Clust=( 0.67 0.33 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

89

SRD1_YPD
(ROC)
74 regulated

16%, 2%
1.3e-02
(pic) (net)

16%, 2%
1.3e-02
(pic) (net)

8%, 1%
1.6e-01
(pic) (net)
Clust=( 0.59 0.41 )

16%, 2%
1.6e-02
(pic) (net)
Clust=( 0.29 0.71 )

90

STB1_YPD
(ROC)
84 regulated

28%, 6%
1.6e-07
(pic) (net)

16%, 4%
5.2e-04
(pic) (net)

36%, 7%
8.6e-10
(pic) (net)
Clust=( 0.18 0.82 )

60%, 11%
9.1e-20
(pic) (net)
Clust=( 0.62 0.38 )

91

STE12_14hr_Butanol
(ROC)
197 regulated

3%, 7%
3.0e-02
(pic) (net)

3%, 7%
3.2e-02
(pic) (net)

3%, 6%
4.6e-02
(pic) (net)
Clust=( 0.50 0.50 )

11%, 16%
5.9e-10
(pic) (net)
Clust=( 0.41 0.59 )

F$STE11_01
Found

92

STE12_90min_Butanol
(ROC)
147 regulated

8%, 10%
2.6e-05
(pic) (net)

9%, 10%
6.2e-06
(pic) (net)

6%, 8%
6.8e-04
(pic) (net)
Clust=( 0.55 0.45 )

19%, 17%
2.8e-15
(pic) (net)
Clust=( 0.41 0.59 )

F$STE12_Q4
Found

93

STE12_Alpha
(ROC)
213 regulated

5%, 9%
7.2e-04
(pic) (net)

7%, 11%
2.3e-05
(pic) (net)

8%, 12%
4.7e-06
(pic) (net)
Clust=( 0.51 0.49 )

11%, 17%
3.4e-10
(pic) (net)
Clust=( 0.57 0.43 )

94

STE12_YPD
(ROC)
130 regulated

3%, 2%
2.2e-01
(pic) (net)

3%, 2%
2.3e-01
(pic) (net)

3%, 2%
1.5e-01
(pic) (net)
Clust=( 0.57 0.43 )

14%, 10%
5.2e-07
(pic) (net)
Clust=( 0.56 0.44 )

95

STP1_YPD
(ROC)
71 regulated

11%, 2%
1.6e-02
(pic) (net)

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

11%, 2%
2.8e-02
(pic) (net)
Clust=( 0.14 0.86 )

23%, 5%
5.7e-05
(pic) (net)
Clust=( 0.50 0.50 )

96

STP2_YPD
(ROC)
68 regulated

18%, 4%
8.2e-04
(pic) (net)

18%, 4%
7.0e-04
(pic) (net)

25%, 6%
1.8e-05
(pic) (net)
Clust=( 0.36 0.64 )

31%, 5%
1.8e-06
(pic) (net)
Clust=( 0.54 0.46 )

97

SUM1_YPD
(ROC)
117 regulated

37%, 23%
1.3e-26
(pic) (net)

38%, 23%
1.3e-27
(pic) (net)

59%, 24%
5.4e-45
(pic) (net)
Clust=( 0.73 0.27 )

51%, 25%
2.8e-39
(pic) (net)
Clust=( 0.14 0.86 )

98

SWI4_YPD
(ROC)
224 regulated

28%, 36%
4.2e-38
(pic) (net)

28%, 35%
1.0e-37
(pic) (net)

22%, 24%
6.2e-24
(pic) (net)
Clust=( 0.33 0.67 )

36%, 33%
1.5e-47
(pic) (net)
Clust=( 0.52 0.48 )

99

SWI5_YPD
(ROC)
156 regulated

31%, 11%
2.8e-19
(pic) (net)

32%, 11%
6.1e-20
(pic) (net)

37%, 12%
6.1e-24
(pic) (net)
Clust=( 0.77 0.23 )

50%, 16%
1.0e-38
(pic) (net)
Clust=( 0.34 0.66 )

#

NAME

PSSM
(sens,spec,pval)

Tree
(sens,spec,pval)

Mixture of PSSMs
(sens,spec,pval)

Mixture of Trees
(sens,spec,pval)

TRANSFAC

100

SWI6_YPD
(ROC)
192 regulated

21%, 17%
1.5e-16
(pic) (net)

26%, 20%
3.5e-22
(pic) (net)

24%, 19%
1.3e-19
(pic) (net)
Clust=( 0.39 0.61 )

39%, 23%
6.6e-36
(pic) (net)
Clust=( 0.39 0.61 )

101

THI2_Thi-
(ROC)
119 regulated

8%, 6%
9.1e-04
(pic) (net)

13%, 10%
1.0e-06
(pic) (net)

11%, 9%
9.8e-06
(pic) (net)
Clust=( 0.35 0.65 )

31%, 16%
8.1e-19
(pic) (net)
Clust=( 0.63 0.37 )

102

YAP1_H2O2
(ROC)
134 regulated

21%, 13%
1.3e-12
(pic) (net)

18%, 15%
1.6e-11
(pic) (net)

12%, 9%
1.7e-06
(pic) (net)
Clust=( 0.46 0.54 )

32%, 13%
1.3e-18
(pic) (net)
Clust=( 0.54 0.46 )

103

YAP1_YPD
(ROC)
101 regulated

15%, 9%
1.2e-06
(pic) (net)

17%, 9%
1.2e-07
(pic) (net)

20%, 10%
1.3e-08
(pic) (net)
Clust=( 0.58 0.42 )

40%, 17%
2.2e-21
(pic) (net)
Clust=( 0.28 0.72 )

104

YAP5_YPD
(ROC)
168 regulated

31%, 43%
5.2e-39
(pic) (net)

35%, 43%
3.1e-45
(pic) (net)

53%, 16%
8.9e-43
(pic) (net)
Clust=( 0.81 0.19 )

63%, 34%
3.0e-76
(pic) (net)
Clust=( 0.71 0.29 )

105

YAP6_YPD
(ROC)
146 regulated

14%, 14%
3.2e-10
(pic) (net)

14%, 14%
4.2e-10
(pic) (net)

12%, 8%
1.3e-06
(pic) (net)
Clust=( 0.43 0.57 )

26%, 21%
1.5e-21
(pic) (net)
Clust=( 0.54 0.46 )

106

YFL044C_YPD
(ROC)
109 regulated

11%, 2%
2.4e-02
(pic) (net)

14%, 3%
2.3e-03
(pic) (net)

7%, 1%
1.7e-01
(pic) (net)
Clust=( 0.84 0.16 )

37%, 5%
2.8e-09
(pic) (net)
Clust=( 0.28 0.72 )

107

YJL206C_YPD
(ROC)
67 regulated

22%, 8%
3.8e-07
(pic) (net)

22%, 9%
2.9e-07
(pic) (net)

40%, 9%
1.2e-12
(pic) (net)
Clust=( 0.34 0.66 )

70%, 16%
1.0e-27
(pic) (net)
Clust=( 0.43 0.57 )

108

ZAP1_YPD
(ROC)
69 regulated

16%, 4%
3.6e-04
(pic) (net)

25%, 6%
9.5e-07
(pic) (net)

20%, 4%
4.3e-05
(pic) (net)
Clust=( 0.40 0.60 )

62%, 13%
5.3e-21
(pic) (net)
Clust=( 0.56 0.44 )

109

ZAP1_Zn
(ROC)
94 regulated

43%, 20%
1.1e-22
(pic) (net)

46%, 16%
2.2e-22
(pic) (net)

43%, 14%
9.6e-20
(pic) (net)
Clust=( 0.38 0.62 )

66%, 18%
1.7e-34
(pic) (net)
Clust=( 0.41 0.59 )