Table 3 Genetic networks in CT drugs-treated OC spheroidsa.
Ntwk | Genes in Ingenuity networksb | Associated pathways | Scorec |
|---|---|---|---|
A. Networks, commonly affected by treatment with all drugs (cisplatin, topotecan and paclitaxel) | |||
1 | ARL2, ARL6IP, ATAD2, BUB1 (includes EG:699), CDKN1A, CEP55, CTH, DEAF1, DTL, EIF5A, FHIT, HES6, HIST1H1B, HNRPA2B1, HOXA10, ING5, KIAA0101, KIF23, KIF2C, NUSAP1, PBK, PKMYT1, PLK1, PRC1, PSAP, RACGAP1, SORT1, SPDEF, TBCD, TUBB3, TUBB2A, UBE2S, UBE2T, UHRF1, VGLL4 | Cell Cycle, Cellular Movement, Cancer | 43 |
2 | BIRC3, BRE, CASP3, CASP7, CEBPE, CSF3, CTSD, DLC1, DNM2, EDA, EIF4B, EIF4G1, EMD, ENO1, FADD, FANCA, GPX4, GRK1, IGF2R, IL17RA, KNTC2, LAMA5, LMNA, MAD1L1, PLSCR1, PRKCE, PTMA, RHO, SNCG, SPBC25, SPTAN1, TNFRSF6B, TRIM63, TXNL5, ZWINT | Cell Death, Connective Tissue Disorders, Cellular Growth and Proliferation | 43 |
3 | ADCY2, AHR, ALCAM, APOE, ASCL2, CASK, CCND1, CDKN2D, COX7A2L, CRYL1, DBP, DKK1, DLG1, DLL4, F11R, FZD1, FZD4, GMNN, KLF5, LDLR, LDLRAP1, LRPAP1, MCM10, MDFI (includes EG:4188), MRAS, PER2, PLXNB2, PPP2CB, PPP2R4, SET, SMARCB1, SMARCD2, SNX17 (includes EG:9784), WNT1, WNT3A | Gene Expression, Lipid Metabolism, Small Molecule Biochemistry | 43 |
4 | AKT2, BRCA1, BRCA2, C5, CA5A, CD151, DDB2, DDIT4, GNB2L1, HMG20B, IFI35, ITGB1, ITGB1BP2, JAK1, LRCH4, NMI, NOV, NRAS, NTN1, PERP (includes EG:64065), PIK4CA, PITPNM1, PPP1R2, PPP1R9B, PTPN11, PTPRM, SERPINH1, SH2D1A (includes EG:4068), SLAMF1, SLC7A8, SNAI2, TMED9, TNFAIP2 (includes EG:7127), XRCC6, YWHAB | Cell Death, Cancer, Cell Cycle | 43 |
5 | ACAA1, ACOT8, B2M, CTSL2, DHCR24, GADD45B, HIPK2, HLA-A, HLA-B, HLA-E, HLA-F, HMGA1, IL22RA2, INSR, MGLL, MVK, MYBBP1A, NALP12, PCNA, PFDN6, PIK3R2, PKLR, POLDIP2, PPARA, PPARGC1B, PSMB8, PTPRG, RFX1, RFXAP, RRM1, SFRS5, SNX15, SURF6, TOMM40, TUB | Nutritional Disease, Cancer, Lipid Metabolism | 43 |
B. Networks, affected by cisplatin treatment | |||
1 | BRCA1, CEBPE, CLU, DDIT4, ECE1, EEF1D, ENO1, EPPB9, GATA3, HIPK2, LDLR, LDLRAP1, LTBP3, MAD1L1, MAPKAPK2, MGMT, MSH2, MXD4, PDZK1IP1, PERP (includes EG:64065), PKIG, PLSCR1, PRKCG, PSMC3, PSMD12, RAG2, RHO, SMAD3, SPHK1, STOML2, TGFB1, TGIF, TMEPAI, TNFAIP2 (includes EG:7127), XRCC6 | Cell Cycle, Cancer | 51 |
2 | ATAD2, CDC2, CDKN1A, CHAF1B, DKFZP762E1312, DNMT1, DTL, EXO1, FHIT, HES6, HOXA10, ING5, KIAA0101, MCM2, MCM3, MCM4, MCM10, MYBBP1A, NUSAP1, PBK, PCNA, PIP5K1C, PKMYT1, PSAP, RACGAP1, RRM1, RRM2, RUVBL2, TYMS, UBE2A (includes EG:7319), UBE2S, UBE2T, UHRF1, VGLL4, WDHD1 | DNA Replication, Recombination, and Repair, Cancer | 51 |
3 | APAF1, APIP, AVEN, BCL2A1, BDNF, BIN1, BIRC1, CASP3, CASP7, CSH2, CTSD, DBNL, DEDD, DFFA, DLC1, DNM2, EIF4G1, EIF4G3, FADD, GAS2, GPX4, HCRT, HSH2D, ITGB3BP, LTBR, MAP2K5, PDE4A, PINK1, PRKAA2, PRKCZ, PSAP, SNCG, STK11, TGFA, TNFRSF6B | Cell Death, Cancer, Hematological Disease | 21 |
4 | BRD2, C19ORF2, CREB1, CYP11A1, EP300, EWSR1, EXOSC6, FUSIP1, GAS2L1, HLA-G, HSPA4L, ITM2C, LSM7, MYH13, MYOD1, NFYB, NUDT2, POLR1A, POLR2A, POLR2E, POLR2F, RRN3, SENP1, SIAHBP1, SUPT3H, TAF1C, TBP, TEAD2, TEAD4, TKT, TNNC1, TNNI2, TNNT2, TRERF1, VGLL1 | Gene Expression, Cell Cycle, Skeletal and Muscular System Development and Function | 20 |
5 | ALAS1, ALPP, ARPC5, CD244, CD2BP2, CTH, CUGBP2, DNAJB5, EDF1, EGR2, EPS8L2, ERG, FOS, GRM4, HDLBP, HLA-B, HOXA9, IL1RL1, JUB, JUN, KEAP1, NFE2L2, NIPSNAP1, NTS (includes EG:57303), PMP22, RPS9, SDCBP, SKIV2L, SNCG, SNRPB, SOS1, USP1, WBP4, WDR90, WT1 | Gene Expression, Organismal Injury and Abnormalities | 18 |
C. Networks, affected by topotecan treatment | |||
1 | ARL6IP, ASPM, ATAD2, CDKN1A, COG1, COG5, CRI2, DDB2, DEAF1, DLG7, FHIT, H2AFZ, HES6, HIST1H1B, HNRPA2B1, KIF2C, KLF5, LIG3, MLLT1, NEIL1, NUSAP1, PARP2, PLK2, PSAP, RACGAP1, SET, SPDEF, SUPT16H, TRIM44 (includes EG:54765), UBE2C, UBE2D1, UBE2S, UBE2T, UHRF1, VGLL4 | DNA Replication, Recombination, and Repair, Cell Cycle, Cellular Compromise | 41 |
2 | ADCY2, ADCY5, AKT1, ASCL2, CCL19, CCND1, CDH2, DKK1, DLC1, DLG1, DLG2, DLL4, FZD1, FZD4, GNAI1, GNB1, GNB2L1, H2AFX, MDFI (includes EG:4188), MRAS, NEUROG1, NEUROG3, NRAS, PRKAG1, PRKAR1A, PTPRM, RASSF1, ROBO1, SEMA3C, SRGAP1, TBCD, TUBB3, TUBB2A, WNT1, WNT3A | Cellular Movement, Cancer, Reproductive System Disease | 41 |
3 | AMPH, BRE, CABIN1, CALM1, CASP3, DAPK1, DDEF1, DNM2, DOCK1, EIF4B, EIF4G1, EIF4G3, ENO1, EPN1, EPS15, GNLY, GRK1, LMNA, MAP4K3, PTK2, PTMA, RHO, RIT2, SNCG, SPHK1, SPTAN1, SPTBN1, STK3, SYNE2, TNFRSF6B, TPD52L1, TPD52L2, TRIO, TXNL5, WASF1 | Cellular Assembly and Organization, Cellular Function and Maintenance, Cellular Movement | 41 |
4 | ALDOA, ANP32B, B2M, BRF1, CALR, CAMK1, CKB, CLIC4, CORO1A, ELAVL1, FN1, GABARAP, HLA-A, HLA-B, HLA-E, IGF1R, ITGB5, ITGB3BP, ITSN1, KPNA2, KRT8, MAPK7, MEF2A, NALP12, NTN1, NUMB, PTPN11, PTPN3 (includes EG:5774), RAB1A, RAN, SLC2A4RG, SND1 (includes EG:27044), VCL, YWHAB, ZAK | Protein Trafficking, Cell Death, Molecular Transport | 41 |
5 | ACTL6A, ACTL6B, ARID1B (includes EG:57492), CCNB2, CDC2, CDK8, CEP170, CGA, CTSL2, GMNN, HMGA2, IFITM2, IFNGR1, INSR, ISGF3G, JAK1, MED25, NEK2, PKMYT1, PLK1, PLXNB2, PRKCZ, PSMA4, PSMB7, PTPRG, PTTG1, RAD51AP1, RNF103, SFRS5, SLC9A3R1, SMARCB1, SMARCD2, SNX15, SURF6, TUB | Cell Cycle, Cellular Assembly and Organization, Cancer | 41 |
D. Networks, affected by paclitaxel treatment | |||
1 | BAG5, CTNNB1, CTNNBIP1, FZD8, GSTP1 (includes EG:2950), H2-ALPHA, JRK, K-ALPHA-1, KIF23, KLK2, LOC112714, LRP6, MDFI (includes EG:4188), MRPL13, MT3, MYF5, PARK2, PLK1, PTP4A3, RBP4, SERPINA5, TPT1, TUBA1, TUBA2, TUBA3, TUBA6, TUBA8, TUBB, TUBB1, TUBB3, TUBB4, TUBB2A, TUBB2C, TUBG1, WNT3A | Cancer, Reproductive System Disease, Renal and Urological Disease | 22 |
2 | ALOX5AP, ASAH2, CEBPE, CEBPG, DDIT3, DHPS, DNAJB5, DUSP9 (includes EG:1852), EIF4G1, ELK4, ERN1 (includes EG:2081), G6PD, GCLC, GCLM, IL3, IMPDH2, LAT, LCN2, MAPK12, MKNK1, MKNK2, MMP8, MT2A, NFE2L2, PRG2 (includes EG:5553), RPS6KA5 (includes EG:9252), SLC5A5, SLK, TALDO1, TDRD7, TGIF, TLR9, TNF, WNT10A, ZBTB17 | Drug Metabolism, Molecular Transport, Small Molecule Biochemistry | 19 |
3 | ARPC1A, ARPC1B, BAX, BIRC6, CCNL2, CXCL13, DDIT4, EIF5A, FFAR3, GATA3, GPR44, HLA-A, HLA-E, HNRPA2B1, HOXC11, HSD17B1, ING5, JMY, LETMD1, LMNA, LTB, LTBP1, MDH1, MDM4, NALP12, PEG3 (includes EG:5178), PPP1R13B, PYCARD, RALY, SERPINB5, STK11, TBX21, TP53, TP53INP1, VHL | Cancer, Cell Death, Skeletal and Muscular Disorders | 19 |
4 | AHNAK, ANP32B, BAK1, C19ORF10, CAMP, DBP, DDIT3, ELAVL1, ENO2, FCGR2A, FCGR2B, HLA-C, HNRPA2B1, HRAS, IFI202B, IFNG, IL6, IL24, IL1RL1, LGALS1, LY6E, MOG, PLCE1, PSMB9, PSMB10, PTMA, S100A10, SDHA, SIRPA, TAP1, TFG, TNFRSF10B, TNFRSF6B, TRIM21, TTC28 | Connective Tissue Disorders, Inflammatory Disease, Cell Death | 17 |
5 | ATF6, ATP5B, BZRAP1, COL1A1, COX4I2, COX5B, COX6A1, COX6A2, COX6B1, COX6B2, COX7A2L, COX7B, COX8C, CREBL1, DBI, GATAD2B, HDAC1 (includes EG:3065), ITM2C, LY6A, MBD3 (includes EG:53615), MBD3L1, MRPL12, MT1A, MYC, NFYB, PLK1, PRRG2, RAB3D, RIMS1, RIMS2, TRAM2, TSPO, TXNIP, UBE2S, ZBTB16 | Cancer, Gene Expression, Tumor Morphology | 17 |