Table 4.
Functional annotations with over-representation of mutations in patients responding or not responding to treatment, children or adults, and biopsy or surgical specimen, 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 (%) | Dataset | Group with significant enrichment |
|---|---|---|---|---|
| Responders vs. nonresponders | ||||
| CD28 co-stimulation | SRC, PIK3R1 | p < 5 | Reactome | Responders |
| Cell cycle progression: G2/M checkpoint | POLE, CHEK1, NOTCH2, BRCA2 | FDR < 25 | Reactome | Responders |
| Vesicle-mediated transport | TSC2, AKT3, AKT1 | FDR < 25 | Reactome | Non-responders |
| Tumor biopsy vs. surgical specimen after neoadjuvant chemotherapy | ||||
| Regulation of PTEN gene transcription | TP53 | FDR < 25 | Reactome | Surgical specimen |
| mTOR signaling | AKT1 TSC1 | p < 5 | Reactome | Surgical specimen |
| PTEN regulation | AKT1 TP53 | p < 5 | Reactome | Surgical specimen |
| Adults vs. children | ||||
| UV response: upregulated genes | SRC, PIK3R1 | FDR < 25 | Hallmark | Adults |
| Cell cycle | ATM, ATR, MRE11, AKT3, MLH1, CCND1, AKT2, MAX, CDKN2A, BRCA2, RAD50 | p < 5 | Reactome | Children |
| DNA repair | BRCA1, MSH6, MSH2, ATM, ATR, MRE11, FANCI, MLH1, PMS2, ERCC2, BRCA2, RAD50 | p < 5% | Reactome | Children |
| Transcriptional regulation by TP53 | BRCA1, MSH2, ATM, ATR, MRE11, AKT3, FANCI, MLH1, PTEN, AKT2, PMS2, CDKN2A, ERCC2, RAD50 | p < 5% | Reactome | Children |
FDR – false discovery rate