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Table 2 Prognostic gene lists rely on genes correlated with the first (cell cycle) principal component variable1.

From: Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists

  

Intercept adjusted

PC1 adjusted

PC2 adjusted

Data set

Gene list

Good/Poor2

HR (p-value)

Good/Poor2

HR (p-value)

Good/Poor2

HR (p-value)

NKI2

       
 

70 Gene

91/174

5.8 (< 0.0001)

30/235

1.2 (0.67)

90/175

5.7 (< 0.0001)

 

Wang 76-gene (ER+)

85/60

4.5 (< 0.0001)

44/101

0.9 (0.84)

89/56

2.7 (0.005)

 

Wang 76-gene (ER-)

6/29

0.9 (0.88)

5/30

1.2 (0.78)

8/27

0.5 (0.25)

 

Wound Signature

74/221

4.1 (0.0002)

27/268

1 (0.93)

73/22

3.9 (0.0002)

 

Sotiriou Grade

92/203

4.7 (< 0.0001)

25/270

0.8 (0.8)

91/204

4.7 (< 0.0001)

 

Naderi

131/104

2.5 (0.0006)

123/112

0.4 (0.003)2

128/107

2.4 (0.0014)

KJX64/KJ125

       
 

70 Gene

38/111

2.8 (0.03)

15/134

0.7 (0.4)

39/110

2.9 (0.03)

 

Wang 76-gene (ER+)

53/36

1.6 (0.32)

35/54

1.2 (0.7)

61/28

1.8 (0.24)

 

Wang 76-gene (ER-)4

14/5

n/a

16/3

n/a

12/7

n/a

 

Sotiriou Grade

46/143

2.9 (0.03)

35/154

1.7 (0.24)

46/143

2.7 (0.03)

 

Naderi

71/56

3.9 (0.004)

69/58

1.6 (0.24)

72/55

3.9 (0.004)

Wang

       
 

70 Gene

49/197

2.6 (0.005)

22/224

0.9 (0.41)

44/202

2.3 (0.015)

 

Wang 76-gene (ER+)

45/84

6.3 (0.0005)

30/99

2 (0.11)

49/80

5.6 (0.0003)

 

Wang 76-gene (ER-)

26/16

11.7 (0.0001)

29/13

8.2 (0.0001)

15/27

4.9 (0.03)

 

Sotiriou Grade

57/229

2.5 (0.007)

21/265

0.7 (0.25)

49/237

2 (< 0.0001)

 

Naderi

106/110

2.4 (0.0008)

105/111

0.9 (0.66)

105/111

3.1 (< 0.0001)

  1. 1. Hazard ratios (HR) represent the change in risk for tumors classified as having a poor prognosis versus tumors classified as having a good prognosis using a univariate proportional hazards analysis. Gene expression data were independently adjusted using simple linear regression analysis for either an intercept only, the principal component representing the first correlated gene cluster identified (PC1) or the second correlated gene cluster identified (PC2) in each data set. Univariate HRs that are significantly (p < 0.05) greater than 1 are shown in bold.
  2. 2. Values in the Good/Poor column indicate the number of tumors assigned to the good and poor prognosis groups, respectively. The total number of tumors per gene list will vary depending upon the number of tumors used in training sets.
  3. 3. The fact that this HR is significantly less than 1 indicates that the classifier did not appropriately classify tumors into appropriate good and poor prognosis groups.
  4. 4. There were too few events among good and poor prognosis groups to perform statistical analyses in the KJX64/KJ125 data set.
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BMC Medical Genomics

ISSN: 1755-8794

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