Table 2.
Frequency of Gene Alterations in Each Pathway.
| Frequency (%) | Frequency (%) | ||||||
|---|---|---|---|---|---|---|---|
| TCGA | This study | TCGA | This study | ||||
| (N = 216) | (N = 100) | (N = 216) | (N = 100) | ||||
| Transcription factor/regulator | 2.6 | 0.0 | GATA3 | MAPK signaling | 26.3 | 12.0 | KRAS |
| 0.9 | 0.0 | EP300 | 11.8 | 2.0 | NF1 | ||
| 4.0 | 0.0 | TAF1 | 1.8 | 0.0 | MAP3K1 | ||
| 0.4 | 0.0 | RUNX1 | 6.6 | 5.0 | BRAF | ||
| 3.5 | 1.0 | WT1 | 1.8 | 0.0 | NRAS | ||
| 0.4 | 0.0 | FOXA1 | 1.3 | 0.0 | MAP2K4 | ||
| 0.4 | 0.0 | CBFB | PI(3)K signaling | 4.4 | 6.0 | PIK3CA | |
| 1.3 | 0.0 | SOX9 | 2.2 | 17.0 | PTEN | ||
| Histone modifier | 6.1 | 17.0 | ARID1A | 1.3 | 4.0 | PIK3R1 | |
| 1.8 | 4.0 | PBRM1 | 11.4 | 0.0 | TLR4 | ||
| 7.9 | 2.0 | SETD2 | 5.3 | 0.0 | PIK3CG | ||
| 4.8 | 1.0 | KDM5C | 0.0 | 2.0 | AKT1 | ||
| 0.9 | 0.0 | KDM6A | TGF-β signaling | 3.1 | 4.0 | SMAD4 | |
| 1.3 | 0.0 | ASXL1 | 0.9 | 4.0 | TGFBR2 | ||
| 2.2 | 0.0 | EZH2 | 2.2 | 1.0 | ACVR1B | ||
| Genome integrity | 51.8 | 40 | TP53 | 0.9 | 1.0 | SMAD2 | |
| 7.9 | 3.0 | ATM | 0.9 | 12.0 | ACVR2A | ||
| 6.1 | 2.0 | ATRX | Wnt/β-catenin | 9.2 | 16.0 | APC | |
| 5.7 | 10.0 | BRCA2 | 3.5 | 5.0 | CTNNB1 | ||
| 5.7 | 0.0 | ATR | 0.9 | 0.0 | AXIN2 | ||
| 2.6 | 0.0 | STAG2 | Proteolysis | 1.3 | 13.0 | FBXW7 | |
| 1.3 | 1.0 | BAP1 | 17.1 | 2.0 | KEAP1 | ||
| 3.5 | NA | BRCA1 | 0.4 | 0.0 | SPOP | ||
| 1.3 | 0.0 | ERCC2 | Splicing | 2.2 | 0.0 | SF3B1 | |
| RTK signaling | 11.4 | 48.0 | EGFR | HIPPO signaling | 1.3 | 2.0 | CDH1 |
| 4.0 | 1.0 | FLT3 | DNA methylation | 4.0 | 0.0 | DNMT3A | |
| 8.8 | 2.0 | EPHA3 | 3.1 | 0.0 | TET2 | ||
| 7.5 | 1.0 | ERBB4 | Metabolism | 0.9 | 0.0 | IDH1 | |
| 6.6 | 2.0 | PDGFRA | 0.4 | 1.0 | IDH2 | ||
| 9.7 | 0.0 | EPHB6 | NFE2L | 2.2 | 2.0 | NFE2L2 | |
| 3.1 | 0.0 | FGFR2 | Protein phosphatase | 4.6 | 0.0 | PPP2R1A | |
| 1.8 | 3.0 | KIT | TOR signaling | 7.5 | 1.0 | MTOR | |
| 0.4 | 2.0 | FGFR3 | 8.8 | 15.0 | STK11 | ||
| Cell cycle | 6.6 | 17.0 | CDKN2A | Other | 3.1 | 0.0 | NOTCH1 |
| 5.3 | 22.0 | RB1 | 5.3 | 0.0 | USP9X | ||
| 3.1 | 1.0 | CDK12 | 0.9 | 0.0 | NPM1 | ||
| 1.8 | 19.0 | CDKN1B | 10.5 | 1.0 | HGF | ||
| 0.9 | 1.0 | CCND1 | 1.8 | 0.0 | AR | ||
| 0.4 | 0.0 | CDKN1A | |||||
| 0.0 | 0.0 | CDKN2C | |||||
| NA | 32.0 | CDKN2B | |||||
Bolded entries represent those genes for which the frequency of alteration was significantly different between TCGA and the present study; N, number; NA, not available.