Table 1.
Genes significantly differentially expressed in tumors.
| (A) Genes Upregulated in Tumors. | |
| Pathway | Genes |
| Apoptosis | BCL2L1, CASP8, MYD88 |
| Base excision repair | APEX2, FEN1, NEIL3, PARP1, SMUG1, UNG |
| Base excision repair—Translesion Synthesis—Cell Cycle and Signaling | PCNA |
| Cell Cycle and Signaling | AURKA, BUB1B, CDKN2A, KRAS, RAD21, RM12, SUMO3 |
| Checkpoint Activation | H2AFX |
| Checkpoint Activation—Cell Cycle and Signaling | CHEK1/2 |
| Homologous Recombination and Fanconi Anemia | BRIP1, BLM, BRCA2, FANCD2, FANCG, FANCI, GEN1, RAD51, RAD54L, UBE2T, USP1, XRCC2, XRCC3 |
| Independent Repair Enzymes/Polymerases | DNA2, POLQ |
| Independent Repair Enzymes/Polymerases–Base excision repair | POLD1, POLD4, POLE2 |
| Independent Repair Enzymes/Polymerases—Cell Cycle and Signaling | MAD2L2 |
| Independent Repair Enzymes/Polymerases–Nucleotide Excision Repair | POLR2D, POLR2H |
| Independent Repair Enzymes/Polymerases–Translesion Synthesis | HLTF |
| Mismatch Repair | MSH2 |
| Mismatch Repair–Translesion Synthesis | RFC4 |
| Non-homologous End Joining—Cell Cycle and Signaling | PRKDC |
| Translesion Synthesis | RAD18 |
| Housekeeping | SF3FA3 |
| (B) Genes downregulated in tumors. | |
| Pathway | Genes |
| Apoptosis | AKT3, BCL2, NFKB2, PIK3R1 |
| Base Excision Repair | NEIL1, NEIL2, OGG1 |
| Cell Cycle and Signaling | ABL1, CCND2, CDKN1A, EGFR |
| Checkpoint Activation | TIPIN |
| Homologous Recombination and Fanconi Anemia | RAD51B, WRN |
| Independent Repair Enzymes/Polymerases | ALKBH3, CRY1, POLK, REV1 |
| Independent Repair Enzymes/Polymerases–Translesion Synthesis | POLI |
| Mismatch Repair | MSH3 |
| Non-homologous End Joining | LIG4 |
| Nucleotide Excision Repair | XPA |
| Nucleotide Excision Repair—Apoptosis | PTEN |
| Housekeeping | COG7, NUBP1 |