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Table 5 Associations between Clusters #1–3 and individual genes using the NKI295 sample set

From: EGFR associated expression profiles vary with breast tumor subtype

  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
  1. 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.
  2. *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.
  3. a the statistically significant association was also significant in the UNC data set (p < 0.0025).
  4. b the association was nominally significant in the NKI dataset (p < 0.05), but significant in the UNC dataset (p < 0.0025).
  5. c the association was significant in the NKI dataset (p < 0.0025), but nominally significant in the UNC dataset (p < 0.05).
  6. d the association was nominally significant in both datasets (p < 0.05).
  7. e the association was significant in UNC dataset (p < 0.0025).
  8. f the association was nominally significant in the UNC dataset (p < 0.05).
  9. Bonferroni corrected level of significance α = 0.0025