Table 2.
BRCA-related miRNA sponge modules using FN, MCL, LINKCOMM and MCODE methods
| Module methods | Module ID | #miRNA sponges | miRNA sponges |
|---|---|---|---|
| FN | 1 | 14 | MYB, EIF4E, E2F3, CDC25A, DNMT3A, VEGFA, BCL2, CCNE1, ETS1, DNMT3B, BIRC5, KDR, FGF2, CCND3 |
| 2 | 12 | NOTCH1, ZEB1, ZEB2, ZFPM2, TCF7L1, ELMO2, KLHL20, KLF11, CCNE2, DLC1, WASF3, WDR37 | |
| 3 | 7 | NFIA, FOXO1, BDNF, RECK, CREB1, SNAI2, RUNX2 | |
| 4 | 5 | PTEN, KLF4, TIMP2, PPARA, BCL2L11 | |
| 5 | 4 | CDK6, MITF, KRAS, CCND2 | |
| 6 | 3 | SMAD4, TP53INP1, CASP3 | |
| MCL | 1 | 5 | PTEN, KLF4, TIMP2, PPARA, BCL2L11 |
| 2 | 12 | NOTCH1, ZEB1, ZEB2, ZFPM2, TCF7L1, ELMO2, KLHL20, KLF11, CCNE2, DLC1, WASF3, WDR37 | |
| 3 | 10 | EIF4E, E2F3, CDC25A, VEGFA, BCL2, CCNE1, ETS1, BIRC5, FGF2, CCND3 | |
| 4 | 4 | CDK6, MITF, KRAS, CCND2 | |
| 5 | 3 | SMAD4, TP53INP1, CASP3 | |
| 6 | 5 | NFIA, FOXO1, BDNF, RECK, SNAI2 | |
| LINKCOMM | 1 | 4 | MYB, ZEB2, ZEB1, DLC1 |
| 2 | 5 | ZEB1, ZEB2, ZFPM2, KLF11, WDR37 | |
| 3 | 3 | FOXO1, RECK, SNAI2 | |
| 4 | 4 | E2F3, CDC25A, CCNE1, CCND3 | |
| 5 | 7 | PTEN, ZEB1, ZFPM2, TCF7L1, KLHL20, KLF11, WDR37 | |
| 6 | 3 | CDC25A, BCL2, CCNE1 | |
| 7 | 5 | PTEN, TIMP2, KLF4, PPARA, BCL2L11 | |
| 8 | 4 | EIF4E, E2F3, BIRC5, FGF2 | |
| 9 | 6 | E2F3, MYB, ZEB2, CCNE2, TCF7L1, KLF11 | |
| 10 | 4 | NOTCH1, ZEB1, ZEB2, ETS1 | |
| 11 | 3 | VEGFA, E2F3, ETS1 | |
| 12 | 7 | ZEB1, ZEB2, ZFPM2, TCF7L1, KLHL20, KLF11, DLC1 | |
| MCODE | 1 | 25 | CDK6, NFIA, EIF4E, DNMT3A, MITF, BDNF, PIM1, KLF4, CREB1, SMAD4, SMAD3, KRAS, CCND2, TIMP2, DNMT3B, TWIST1, BIRC5, KDR, FGF2, PPARA, RUNX2, TP53INP1, CASP3, SMAD2, BCL2L11 |
| 2 | 24 | MYB, PTEN, FOXO1, NOTCH1, ZEB1, ZEB2, ZFPM2, E2F3, CDC25A, TCF7L1, RECK, VEGFA, ELMO2, BCL2, KLHL20, KLF11, CCNE2, CCNE1, ETS1, DLC1, SNAI2, WASF3, WDR37, CCND3 |