Table 5

Associations between Clusters #1–3 and individual genes using the NKI295 sample set

Cluster 1

Cluster 2

Cluster 3




%

p-val

%

p-val

%

p-val


EGFR

39%

0.1783

43%

0.0091b

38%

0.15

HER2

26%

0.0017

25%

<0.0001c

24%

<0.0001a

HER4*

21%

<0.0001

12%

<0.0001

18%

<0.0001

TGFA

40%

0.0665

48%

0.0002

47%

0.0021

AREG

22%

0.0007c

23%

<0.0001a

28%

0.064f

EGF

35%

0.1380

25%

0.0691

27%

0.033d

CRYAB

35%

0.3214f

38%

0.0524

38%

0.0013

KRAS amplicon

38%

0.1973e

52%

<0.0001c

63%

<0.0001a

KRAS gene

27%

0.0022a

31%

0.8795

36%

0.14e

HRAS

48%

<0.0001c

51%

<0.0001

47%

0.0018

NRAS

45%

0.0362

56%

<0.0001c

59%

<0.0001a

PIK3ca

22%

0.0032b

27%

0.1415e

30%

0.33e

PIK3R1

24%

0.0009a

20%

<0.0001a

19%

<0.0001

AKT1

41%

0.0112

39%

0.0899

34%

0.36

AKT2*

40%

0.0519

37%

0.3524

33%

0.94

AKT3

26%

0.0004

33%

0.1569

35%

0.64f

MEK1

39%

0.0335

47%

0.0032d

48%

<0.0001

MEK2

58%

<0.0001a

44%

0.0113d

36%

0.55f

ERK1

37%

0.0718e

23%

0.0009c

19%

<0.0001a

ERK2

39%

0.0238

37%

0.3457e

36%

0.46e


Chi-squared analyses were used to identify associations between the high expression of the individual EGFR-activation profiles for each cluster (top 1/3) and the expression of individual genes categorized as high (top 1/3). The % of tumors with the high expression of each cluster and that show the high expression of the individual gene is shown.

*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 dataset.

a the statistically significant association was also significant in the UNC data set (p < 0.0025).

b the association was nominally significant in the NKI dataset (p < 0.05), but significant in the UNC dataset (p < 0.0025).

c the association was significant in the NKI dataset (p < 0.0025), but nominally significant in the UNC dataset (p < 0.05).

d the association was nominally significant in both datasets (p < 0.05).

e the association was significant in UNC dataset (p < 0.0025).

f the association was nominally significant in the UNC dataset (p < 0.05).

Bonferroni corrected level of significance α = 0.0025

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

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