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Table 2 Heterochrony in module-specific transcription factors.

From: Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes

 

Gene (Alias)

P

R H 1 2 ¯

R H 0 2 ¯

Sig. F -tests (Prop.)

Distortion

Module 1

YHR206W (Skn7)

0.06567o

0.591

0.138

36 (0.80)

77.48

 

YPL089C (Rlm1)

0.07051o

0.605

0.142

35 (0.78)

75.80

 

YNL309W (Stb1)

0.06356o

0.616

0.146

36 (0.80)

74.13

 

YNL216W (Rap1)

0.02399*

0.624

0.175

33 (0.73)

73.92

 

YLR403W (Sfp1)

0.01056*

0.653

0.200

36 (0.80)

73.46

 

YDR207C (Ume6)

0.01626*

0.532

0.153

27 (0.60)

63.20

 

YPR104C (Fhl1)

0.0015**

0.547

0.120

28 (0.62)

59.81

Module 2

YKL112W (Abf1)

0.025*

0.629

0.201

33 (0.73)

68.51

 

YIL131C (Fkh1)

0.04142*

0.649

0.151

35 (0.78)

62.44

Module 3

YOL028C (Yap7)

0.09046o

0.659

0.163

36 (0.80)

77.63

 

YDR123C (Ino2)

0.03916*

0.585

0.134

33 (0.73)

76.02

 

YOR372C (Ndd1)

0.01219*

0.592

0.120

34 (0.76)

73.02

 

YNL068C (Fkh2)

0.00457**

0.601

0.119

34 (0.76)

71.61

 

YER040W (Gln3)

0.00459**

0.593

0.161

29 (0.64)

70.99

 

YMR043W (Mcm1)

0.01094*

0.672

0.203

40 (0.89)

69.36

 

YGL237C (Hap2)

0.00053***

0.537

0.138

22 (0.49)

69.01

 

YML007W (Yap1)

0.03816*

0.603

0.136

35 (0.78)

62.86

Module 4

YOR028C (Cin5)

0.03329*

0.582

0.165

29 (0.64)

87.10

 

YPL202C (Aft2)

0.07004o

0.579

0.092

34 (0.76)

75.80

 

YDL056W (Mbp1)

0.05184o

0.588

0.158

33 (0.73)

73.87

 

YGL071W (Rcs1)

0.02813*

0.581

0.115

33 (0.73)

73.42

 

YDL106C (Pho2)

0.01764*

0.569

0.143

27 (0.60)

61.63

Module 5

YPR065W (Rox1)

0.06635o

0.666

0.185

35 (0.78)

80.97

 

YBR049C (Reb1)

0.04439*

0.682

0.206

37 (0.82)

80.96

 

YDR423C (Cad1)

0.05867o

0.574

0.119

31 (0.69)

75.47

 

YHR178W (Stb5)

0.09263o

0.626

0.166

37 (0.82)

70.27

 

YMR037C (Msn2)

6.0 ×10-5***

0.597

0.183

35 (0.78)

72.13

 

YMR070W (Mot3)

0.09263o

0.624

0.161

35 (0.78)

60.97

 

YKL062W (Msn4)

0.02334*

0.706

0.242

36 (0.80)

54.91

Module 6

YNL216W (Rap1)

0.05212o

0.624

0.175

33 (0.73)

73.92

 

YJR060W (Cbf1)

0.00544**

0.605

0.140

35 (0.78)

73.15

 

YIR018W (Yap5)

0.00379**

0.527

0.110

27 (0.60)

70.80

 

YDL020C (Rpn4)

0.08764o

0.641

0.185

30 (0.67)

70.10

 

YOR344C (Tye7)

0.03477**

0.663

0.175

38 (0.84)

68.96

 

YKL112W (Abf1)

0.04084*

0.629

0.201

33 (0.73)

68.51

 

YPR104C (Fhl1)

0.02139*

0.547

0.120

28 (0.62)

59.81

Module 7

YBR049C (Reb1)

0.00056***

0.682

0.206

37 (0.82)

80.96

 

YKR099W (Bas1)

0.01578*

0.591

0.163

29 (0.64)

69.26

 

YBL103C (Rtg3)

0.04638*

0.607

0.144

36 (0.80)

67.13

 

YDR043C (Nrg1)

0.08764o

0.637

0.205

33 (0.73)

63.85

 

YDR146C (Swi5)

0.02932*

0.764

0.289

41 (0.91)

63.56

 

YDL106C (Pho2)

0.02567*

0.569

0.143

27 (0.60)

61.63

  1. 2 × 2 TF-module association tables were computed that reflect the number of module-specific genes (n = 1,828) that associate with one of seven timing modules and are regulated by one of 63 transcription factors (TFs). (A subset of 63/117 TFs were used that has at least seven targeted genes.) TF regulatory binding data were obtained from [46] using a cutoff of P < 0.001 and moderate conservation (cons = 1). Fisher's Exact tests were used to evaluate the significance of each TF-module association along with a false discovery rate correction ***indicates FDR < 0.001; **indicates FDR < 0.01; *indicates FDR < 0.05; oindicates FDR < 0.1. In total 37 TFs show significant modular association (FDR < 0.1). Five TFs associate with two modules (Abf1, Fhl1, Pho2, Rap1, Reb1). R H 1 2 ¯ and R H 0 2 ¯ indicate explained CDC-expression variation averaged over 45 strain comparisons, computed by the time-dependent heterochrony or time-independent model, respectively. Sig. F-tests indicates the number (and proportion) of significant F-tests supporting the heterochrony model, among strain comparisons. Distortion is computed as the RMSE of the optimal time transformation curve against a line (α = 1, β = 1, γ = 0), averaged over strain comparisons. Genes are ranked by distortion for each category. The average genome-wide distortion (n = 6.082) is 67.6 with a standard deviation of 8.7.
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Genome Biology

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