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Table 3 Candidate differentially-expressed genes

From: Exploratory differential gene expression analysis in microarray experiments with no or limited replication

RN

ORF Name

Synonyms

CIN

log2(Cy3)

log2(Cy5/Cy3)

RSE

SR

p

p'

p''

q

Up-regulated genes

1

YBR207W

 

427

-0.62

1.06

0.14

7.30

3.30E-13

2.00E-09

2.01E-11

1.11E-10

2

YBR295W

PCA1, PAY2

515

-2.30

0.83

0.16

5.26

1.50E-07

9.13E-04

9.18E-06

2.47E-05

3

YDR264C

AKR1

1186

0.10

0.87

0.17

5.22

1.81E-07

1.10E-03

1.11E-05

2.90E-05

4

YDR270W

CCC2

1192

-2.98

1.19

0.21

5.75

9.09E-09

5.52E-05

5.54E-07

1.62E-06

5

YDR476C

 

1394

-1.87

0.84

0.14

6.08

1.24E-09

7.51E-06

7.55E-08

2.78E-07

6

YDR534C

 

1452

-3.83

3.43

0.25

13.66

0.00E+00

0.00E+00

0.00E+00

0.00E+00

7

YEL065W

SIT1

1528

-0.60

2.46

0.15

16.89

0.00E+00

0.00E+00

0.00E+00

0.00E+00

8

YER145C

FTR1

1692

-0.49

2.25

0.15

15.11

0.00E+00

0.00E+00

0.00E+00

0.00E+00

9

YFL041W

FET5

1778

-0.84

0.94

0.14

6.76

1.54E-11

9.32E-08

9.37E-10

4.05E-09

10

YGL015C

 

1879

-3.40

1.04

0.23

4.53

6.07E-06

3.69E-02

3.71E-04

7.23E-04

11

YGL039W

 

1903

-0.68

1.01

0.14

7.06

1.80E-12

1.10E-08

1.10E-10

5.76E-10

12

YGR065C

 

2189

-0.19

0.76

0.16

4.82

1.49E-06

9.01E-03

9.06E-05

1.80E-04

13

YHL035C

 

2453

-2.20

1.70

0.15

11.07

0.00E+00

0.00E+00

0.00E+00

0.00E+00

14

YHL040C

ARN1

2458

-2.38

2.45

0.16

14.95

0.00E+00

0.00E+00

0.00E+00

0.00E+00

15

YHL047C

 

2465

-4.59

4.19

0.29

14.43

0.00E+00

0.00E+00

0.00E+00

0.00E+00

16

YHR042W

NCP1

2511

0.27

0.72

0.17

4.27

2.00E-05

1.21E-01

1.22E-03

2.01E-03

17

YHR175W

CTR2

2644

-1.38

1.08

0.13

8.32

0.00E+00

0.00E+00

0.00E+00

0.00E+00

18

YJL153C

INO1, APR1

3057

-2.03

0.74

0.15

5.06

4.33E-07

2.63E-03

2.64E-05

6.25E-05

19

YKL220C

FRE2

3507

-3.98

2.78

0.26

10.75

0.00E+00

0.00E+00

0.00E+00

0.00E+00

20

YLL051C

FRE6

3668

-1.44

0.97

0.13

7.55

4.97E-14

3.02E-10

3.03E-12

1.78E-11

21

YLR034C

SMF3

3716

0.04

0.72

0.16

4.41

1.04E-05

6.32E-02

6.35E-04

1.11E-03

22

YLR046C

 

3728

-1.88

0.72

0.14

5.19

2.21E-07

1.34E-03

1.35E-05

3.44E-05

23

YLR056W

ERG3, SYR1

3738

0.92

0.80

0.18

4.47

8.04E-06

4.88E-02

4.90E-04

8.71E-04

24

YLR126C

 

3808

-2.03

1.00

0.15

6.85

8.07E-12

4.90E-08

4.92E-10

2.23E-09

25

YLR136C

TIS11, CTH2

3818

-1.31

0.91

0.13

7.02

2.41E-12

1.46E-08

1.47E-10

7.30E-10

26

YLR205C

 

3885

-2.91

1.19

0.20

5.87

4.47E-09

2.71E-05

2.72E-07

8.47E-07

27

YLR214W

FRE1

3894

-1.18

1.51

0.13

11.62

0.00E+00

0.00E+00

0.00E+00

0.00E+00

28

YMR006C

PLB2

4286

-0.84

0.61

0.14

4.39

1.16E-05

7.06E-02

7.10E-04

1.22E-03

29

YMR011W

HXT2

4291

0.02

0.81

0.16

4.96

7.28E-07

4.42E-03

4.44E-05

1.00E-04

30

YMR058W

FET3

4340

0.42

1.91

0.17

11.10

0.00E+00

0.00E+00

0.00E+00

0.00E+00

31

YMR251W

 

4540

-4.28

1.19

0.27

4.33

1.48E-05

9.00E-02

9.05E-04

1.53E-03

32

YNL237W

YTP1

4856

-4.34

1.25

0.28

4.50

6.86E-06

4.16E-02

4.18E-04

7.95E-04

33

YNL259C

ATX1

4878

-0.06

0.96

0.16

5.95

2.90E-09

1.76E-05

1.77E-07

5.86E-07

34

YNR056C

BIO5

5003

-2.74

1.45

0.19

7.60

3.38E-14

2.05E-10

2.06E-12

1.28E-11

35

YNR060W

FRE4

5007

-3.64

1.22

0.24

5.03

4.96E-07

3.01E-03

3.02E-05

7.00E-05

36

YOL158C

 

5181

-2.76

2.93

0.19

15.28

0.00E+00

0.00E+00

0.00E+00

0.00E+00

37

YOR334W

MRS2

5524

-0.15

0.68

0.16

4.27

1.95E-05

1.18E-01

1.19E-03

1.97E-03

38

YOR381W

FRE3

5571

-2.23

1.77

0.16

11.37

0.00E+00

0.00E+00

0.00E+00

0.00E+00

39

YOR382W

 

5572

-2.86

2.86

0.20

14.42

0.00E+00

0.00E+00

0.00E+00

0.00E+00

40

YOR383C

 

5573

-4.03

4.72

0.26

18.07

0.00E+00

0.00E+00

0.00E+00

0.00E+00

41

YOR384W

FRE5

5574

-3.82

1.56

0.25

6.23

5.11E-10

3.10E-06

3.12E-08

1.29E-07

Down-regulated genes

1

YBR054W

YRO2

273

1.28

-0.95

0.19

-5.12

3.11E-07

1.89E-03

1.90E-05

4.72E-05

2

YBR147W

 

366

-1.68

-0.64

0.13

-4.87

1.13E-06

6.86E-03

6.90E-05

1.40E-04

3

YCL030C

HIS4

547

1.80

-0.87

0.19

-4.50

6.95E-06

4.22E-02

4.24E-04

7.95E-04

4

YDL171C

GLT1

857

-0.59

-0.87

0.15

-5.95

2.81E-09

1.70E-05

1.71E-07

5.86E-07

5

YEL039C

CYC7

1502

-1.34

-0.69

0.13

-5.31

1.14E-07

6.91E-04

6.95E-06

1.92E-05

6

YER174C

GRX4

1721

1.09

-0.92

0.18

-5.06

4.31E-07

2.61E-03

2.63E-05

6.25E-05

7

YFL014W

HSP12, GLP1, HOR5

1751

1.18

-0.91

0.18

-4.95

7.57E-07

4.60E-03

4.62E-05

1.02E-04

8

YFR030W

MET10

1836

0.54

-1.01

0.17

-5.79

7.61E-09

4.62E-05

4.64E-07

1.40E-06

9

YFR055W

 

1862

-0.74

-0.69

0.14

-4.90

1.00E-06

6.07E-03

6.11E-05

1.27E-04

10

YGL009C

 

1873

4.10

-1.27

0.23

-5.58

2.54E-08

1.54E-04

1.55E-06

4.40E-06

11

YGL117W

 

1979

1.05

-1.25

0.18

-6.85

8.05E-12

4.89E-08

4.91E-10

2.23E-09

12

YGR088W

CTT1

2212

-1.93

-0.63

0.14

-4.48

7.50E-06

4.55E-02

4.57E-04

8.34E-04

13

YGR286C

BIO2

2409

0.97

-1.10

0.18

-6.11

1.09E-09

6.61E-06

6.65E-08

2.54E-07

14

YHL021C

 

2440

-0.19

-0.97

0.16

-6.17

7.25E-10

4.40E-06

4.42E-08

1.76E-07

15

YJR137C

ECM17, MET5

3263

0.42

-0.85

0.17

-4.92

8.71E-07

5.28E-03

5.31E-05

1.12E-04

16

YKL148C

SDH1

3436

-1.12

-0.77

0.13

-5.91

3.56E-09

2.16E-05

2.17E-07

6.97E-07

17

YLL041C

SDH2

3658

-0.49

-0.90

0.15

-6.05

1.50E-09

9.10E-06

9.15E-08

3.25E-07

18

YLR304C

ACO1, GLU1

3985

2.05

-0.88

0.20

-4.48

7.56E-06

4.59E-02

4.61E-04

8.34E-04

19

YMR021C

MAC1, CUA1

4301

-0.43

-1.83

0.15

-12.17

0.00E+00

0.00E+00

0.00E+00

0.00E+00

20

YOR356W

 

5546

-0.03

-0.80

0.16

-4.93

8.45E-07

5.13E-03

5.16E-05

1.12E-04

  1. Candidates for differentially-expressed genes in the mac1 cDNA microarray experiment defined as those outside the adjusted supsmu-based 99.998%-STIs (unadjusted p-value ≤ 0.00002). The study monitored transcripts in a mac1 knockout and wild-type S. cerevisiae. RN, row number; ORF name, systematic name for open reading frame; Synonyms, alternative gene names (if any); CIN, case index numbers used in scatter plots to identify data points; log2(Cy3), predictor variable (log base 2 transformed Cy3 intensity value); log2(Cy5/Cy3), log base 2 of Cy5/Cy3 ratio (here ratios are residuals); RSE, residual scale estimator (for data points represented in the table it is based on supsmu non-parametric regression smoother); SR, standardized residuals (log2(Cy5/Cy3) divided by RSE); p, unadjusted p-values based on statistics for two-sided tolerance intervals; p', Bonferroni adjusted p-values using N = 6,068; p'', Bonferroni adjusted p-values using k = 61, q, q-values calculated using qvalue() function [45, 46] (see Figure 24 supporting q-value calibration). p- and q-values are given in scientific notation and 0.00E+00 means that a value was less than 10-16.