Table 3 of Ganguly, Mol Vis 2010; 16:1292-1303. Table 3 of Ganguly, Mol Vis 2010; 16:1292-1303.
Table 3. Canonical Pathways deregulated in RB tumor tissue.
Canonical pathways |
-Log (P-value) |
Ratio of molecules in this data set compared to total number of molecules in reference | Down regulated molecules (compared to total number in the respective pathway) | Upregulated molecules (compared to total number in the respective pathway) | No overlap with data set | Genes |
|---|---|---|---|---|---|---|
| DNA damage response and BRCA1 gene | 12 | 0.472 | 1/53 (2%) | 24/53 (45%) | 28/53 (53%) | BARD1, RBBP8, E2F3, RBL1, SMARCA4, CHEK1, FANCE, RAD51, FANCD2, BRCA1, BLM, E2F2, RBL2, FANCG, PLK1, RPA1, RFC5, MSH2, RFC4, E2F1, MSH6, BRCA2, HLTF, FANCA, RFC3 |
| Aryl hydrocarbon receptor signaling | 6.85 | 0.217 | 18/157 (11%) | 16/157 (10%) | 123/157 (78%) | TRIP11, NFIX, GSTM5, TP73, POLA1, SMARCA4, CHEK1, TGM2, CCNA2, PTGES3 (includes EG: 10728), CCNA1, ALDH1A3, TGFB2, NFE2L2, ALDH6A1, GSTK1, CCNE2, NFIC, TFDP1, GSTM, NQO1, MAPK8, MDM2, NCOA3, RXRG, CCNE1, CCND2, NFIA, E2F1, ALDH3B1, DHFR, GSTO2, ESR1, MCM7 |
| ATM signaling | 5.93 | 0.346 | 0/52 (0%) | 18/52 (35%) | 34/52 (65%) | SMC3, CDC25C, CCNB1, TP73, MAPK8, MDC1, CCNB2, MDM2, CREB3L4, CDC2, SMC1A, CHEK1, RAD51, SMC2, FANCD2, TLK2, BRCA1, CDC25A |
| G2/M DNA damage checkpoint regulation | 5.93 | 0.349 | 2/43 (5%) | 13/43 (30%) | 28/43 (65%) | PRKDC, CDC25C, CCNB1, YWHAB, WEE1, CCNB2, MDM2, PLK1, SKP1, CDC2, SKP2, CHEK1, KAT2B, TOP2A, BRCA1 |
| Mitotic roles of polo-like kinase | 5.93 | 0.306 | 1/62 (2%) | 18/62 (29%) | 43/62 (69%) | KIF23, CDC25C, CCNB1, ESPL1, CDC20, WEE1, PTTG1, PRC1, CDC7, CCNB2, PLK1, CDC23, CDC2, PPP2R5A, SMC1A, PLK4, PKMYT1, KIF11, CDC25A |
| Role of CHK proteins in cell cycle checkpoint control | 5.86 | 0.412 | 0/34 (0%) | 14/34 (41%) | 20/34 (59%) | CDC25C, RPA1, RFC5, E2F3, CDC2, CHEK1, PCNA, RFC4, E2F1, TLK2, BRCA1, E2F2, RFC3, CDC25A |
| Purine metabolism | 5.31 | 0.125 | 12/440 (3%) | 43/440 (10%) | 385/440 (88%) | PRIM1, POLR2D, PRTFDC1, POLA1, ADARB1, POLE, POLD3, PDE7B, PRUNE, RAD51C, AK7, GUCY1B3, GUCY1A3, POLE2, RRM2, ENPP5, PAPSS2, NT5C3, MPP3, POLD2, ATP6V0E1, PPAT, RFC3, DDX39, PDE7A, POLQ, PDE4A, POLR2B, SMARCA4, WRNIP1, RAD51, ENTPD3, ENPP2, BLM, DHX15, ADCY2, DCK, ENTPD1, PAICS, CASK, HSPD1, RFC |
| Molecular Mechanisms of Cancer | 4.64 | 0.156 | 27/372 (7%) | 31/372 (8%) | 314/372 (84%) | TGFBR1, CDKN2C, RBL1, PMAIP1, NFKBIB, BRCA1, E2F2, CDC25A, CCNE2, TFDP1, RALB, RHOJ, AURKA, RASGRF2, DAXX, RHOQ, CCND2, RABIF, GAB1, ARHGEF6, E2F1, MAP2K3, PIK3CD, CFLAR, NOTCH1, TCF4, RALA, BMP2, CTNNA1, PSEN2, MAP3K5, E2F3, CHEK1, CASP6, FANCD2, RHOT1, GNAT2, TGFB2, PRKCE |
| Cell Cycle: G1/S Checkpoint Regulation | 3.68 | 0.254 | 4/59 (7%) | 11/59 (19%) | 44/59 (75%) | CCNE2, RBL2, TFDP1, HDAC2, NRG1, RBL1, E2F3, SKP1, SKP2, CCNE1, CCND2, E2F1, TGFB2, E2F2, CDC25A |
| P53 Signaling | 3.47 | 0.225 | 5/89 (6%) | 15/89 (17%) | 69/89 (78%) | PRKDC, PIK3C2A, TP73, MAPK8, MDM2, PTEN, BIRC5, CHEK1, CCNG1, KAT2B, CASP6, PCNA, CCND2, E2F1, BAI1, AKT3, PIK3CD, LRDD, BRCA1, PMAIP1 |