Table 2. Analysis of Targeted and Immunotherapy Pathways.
| no. of associated proteins in gene ontologya | n umber of proteins in the networkb | median normal abundancec | median adenoma abundancec | median carcinoma abundancec | p value (normal-adenoma)d | p value (adenoma-carcinoma)d | p value (normal-carcinoma)d | |
|---|---|---|---|---|---|---|---|---|
| EGFR signaling | 121 | 58 | 7.061 | 6.665 | 7.058 | 0.01783* | 0.018* | 0.67023 |
| VEGFR signaling | 93 | 49 | 6.662 | 7.383 | 7.608 | 0.84231 | <0.001* | 0.01791* |
| mismatch repair | 38 | 8 | 8.533 | 9.931 | 8.987 | 0.08006 | 1.000 | 0.23395 |
a
Number of human protein search results for GO terms: epidermal growth factor receptor signaling pathway, vascular endothelial growth factor receptor signaling pathway, and mismatch repair.
b
Number of proteins in the Human Cancer Signaling Network, constructed as described in the Materials and Methods.
c
Abundances were calculated from GEO data sets. For further details, see the Materials and Methods. We used median values because the data set distribution, based on Shapiro-Wilk tests, were not considered a normal distribution.
d
On the basis of the results of the normality tests, we used paired Wilcoxon tests to evaluate the significance of the changes in the targeted therapy-associated data.