Table 3.
Functional annotations with over-representation of mutations in all Ewing samples, together with the level of significance and the genes that significantly affect the enrichment statistics calculated by the GSEA program (Reactome or Hallmark)
| Pathway | Genes | Significance (false discovery rate, %) | Dataset |
|---|---|---|---|
| G2/M DNA damage checkpoint | TP53, ATM, CHEK1, ATR, NBN, BRCA1, RAD50 | <25 | Reactome |
| Pre-NOTCH EXPRESSION AND PROCESSING | NOTCH1, TP53, CREBBP, NOTCH2, NOTCH3 | < 25 | |
| DNA repair |
POLE, TP53, BRCA2, ATM, MSH2, MLH1, CHEK1, MSH6, ATR, NBN, BRCA1, RAD50, BAP1, FANCI, FANCA, PALB2 |
< 25 | |
| DNA double-strand break repair | POLE, TP53, BRCA2, ATM, CHEK1, ATR, NBN, BRCA1, RAD50, BAP1 | < 25 | |
| Cell cycle progression: E2F targets (E2F_TARGETS) | POLE, TP53, BRCA2, MSH2, MLH1, CHEK1, NBN, BRCA1, RAD50 | < 25 | Hallmark |
| Cell cycle progression: G2/M checkpoint (G2M_CHECKPOINT) |
POLE, BRCA2, ATRX, NOTCH2, CHEK1 | < 25 | |
| Canonical beta-catenin pathway (WNT_BETA_CATENIN_SIGNALING) |
NOTCH1, TP53, PTCH1 | < 25 | |
| Genes important for mitotic spindle assembly (MITOTIC_SPINDLE) | NF1, BRCA2, NOTCH2, TSC1 | < 25 |