Table 5 |
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|
Associations between Clusters #1–3 and individual genes using the NKI295 sample set |
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|
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 |
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|
Hoadley et al. BMC Genomics 2007 8:258 doi:10.1186/1471-2164-8-258 |
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