Table 4

Chi-square analysis for association of gene expression with subtypes

Basal-like

HER2+/ER-

Luminal A

Luminal B

Normal-like

p-value


# tumors

53

35

123

55

29


Cluster 1a

68%

37%

12%

56%

14%

<0.0001

Cluster 2a

89%

49%

5%

49%

7%

<0.0001

Cluster 3a

77%

51%

11%

47%

0%

<0.0001

EGFRa

68%

20%

27%

18%

41%

<0.0001

HER2a

15%

100%

28%

26%

24%

<0.0001

HER4*

9%

3%

50%

38%

31%

<0.0001

TGFAb

74%

37%

17%

25%

38%

<0.0001

AREGa

3%

34%

43%

35%

41%

<0.0001

EGF

17%

40%

37%

36%

31%

0.23

CRYABa

70%

11%

33%

4%

48%

<0.0001

KRAS amplicona

68%

40%

24%

35%

0%

<0.0001

KRAS genec

32%

37%

33%

38%

21%

0.36

HRASd

32%

66%

17%

64%

7%

<0.0001

NRASa

70%

28%

17%

44%

21%

<0.0001

PIK3CA

30%

17%

36%

36%

41%

0.28

PIK3R1a

21%

14%

42%

25%

55%

0.0012

AKT1a

26%

63%

27%

40%

24%

<0.0001

AKT2*

26%

40%

27%

47%

38%

0.26

AKT3a

51%

14%

39%

9%

45%

<0.0001

MEK1

53%

46%

25%

29%

24%

0.023

MEK2e

42%

43%

25%

42%

24%

0.068

ERK1f

30%

26%

31%

42%

41%

0.49

ERK2g

40%

31%

26%

45%

31%

0.048


Samples were rank ordered into three equal groups and the percentage of each subtype in the highest expression group is reported for the NKI patient data set.

*Note: HER4 could not be assessed in UNC data due to too many missing values; HER3 was not present in the NKI data set; AKT2 was not present in the UNC data set

a associations were also similarly significant in the UNC sample set

b nominally significant in UNC data (p-value = 0.0046)

c nominally significant association in the UNC data (p-value= 0.0051)

d nominally significant in the UNC data (p-value = 0.003)

e nominally significant in the UNC data (p-value = 0.0023)

f significant in the UNC data (p-value = 0.0003)

g significant in the UNC data (p-value = <0.0001)

Bonferroni corrected level of significance α = 0.0022

Hoadley et al. BMC Genomics 2007 8:258   doi:10.1186/1471-2164-8-258

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