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Table 2 Gene set enrichment analysis of 394 ER-positive breast cancers: part 2

From: Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers

  

Comparison

  

LN- over LN+

Grade 3 over grade 1

Grade 3 over grade 2

Grade 2 over grade 1

 

Gene set

NES

Nominal P

FWER P

NES

Nominal P

FWER P

NES

Nominal P

FWER P

NES

Nominal P

FWER P

Modulation of E2 and ER

Estrogen/ER induced

-1.38

0.07

0.47

1.40

0.07

0.45

1.14

0.27

0.78

1.27

0.15

0.63

 

Estrogen/ER repressed

1.35

0.11

0.52

-1.51

0.05

0.28

-1.27

0.16

0.62

-1.21

0.18

0.69

Modulation of oxidative stress

Ox induced

1.14

0.30

0.79

1.44

0.08

0.38

1.55

0.06

0.23

0.78

0.75

0.98

 

Ox repressed

1.03

0.42

0.87

-1.32

0.11

0.57

-1.51

0.03

0.29

-0.88

0.65

0.95

 

Ox-E/ER Ox induced

1.10

0.36

0.82

1.11

0.34

0.80

1.11

0.35

0.82

-0.98

0.46

0.90

 

Ox-E/ER Ox repressed

1.24

0.20

0.69

-1.00

0.44

0.90

-1.34

0.12

0.54

-0.42

1.00

1.00

Modulation of ER and oxidative stress

Ox' induced

1.00

0.44

0.89

1.50

0.05

0.30

1.53

0.06

0.25

0.82

0.70

0.97

 

Ox' repressed

0.99

0.47

0.90

-1.74

0.01

0.06

-1.70

0.01

0.09

-1.19

0.21

0.73

 

Ox'-E/ER Ox induced

1.03

0.42

0.87

0.91

0.52

0.93

0.75

0.77

0.98

-1.43

0.12

0.40

 

Ox'-E/ER Ox repressed

1.24

0.20

0.68

-1.65

0.02

0.12

-1.35

0.13

0.53

-1.48

0.06

0.32

Literaturea

MAPK induced

0.99

0.45

0.90

0.81

0.70

0.98

0.95

0.52

0.92

-0.55

0.96

1.00

 

MAPK repressed

-1.09

0.31

0.81

1.06

0.38

0.84

-1.02

0.44

0.88

1.17

0.27

0.75

 

Luminal markers

1.19

0.32

0.73

-1.71

0.02

0.08

-1.77

0.01

0.05

-0.81

0.65

0.97

 

Sustained estrogen-induced

-1.20

0.23

0.69

1.79

0.00

0.03

1.33

0.11

0.54

1.63

0.02

0.14

 

Proliferation markers

-1.76

0.02

0.06

2.02

0.00

0.00

1.97

0.00

0.00

1.90

0.00

0.01

  1. Gene sets showing nominal enrichment (p < 0.05) are denoted in bold.
  2. Gene sets showing nominal enrichment (P < 0.05) are denoted in bold. aMitogen-activated protein kinase (MAPK) [42], luminal [54], sustained estrogen-induced [43], and proliferation signatures [53] as shown in Additional file 2. E2, estradiol; ER, estrogen receptor; FWER, family-wise error rate; LN, lymph node; NES, normalized enrichment score; Ox-E/ER, oxidant-sensitive estrogen/ER gene signature; PR, progesterone receptor.