Effects of ciglitazone and troglitazone on the proliferation of human stomach cancer cells

Table 3 Biological process of down-regulated genes by troglitazone in SNU-668 cells

Term	Count	Pvalue	Genes
Mitotic sister chromatid segregation	10	1.61E-10	CDCA5, KNTC2, CNAP1, DLG7, NUSAP1, HCAP-G, SMC4L1, CENPE, SMC2L1, ESPL1
Phosphorylation	32	6.36E-04	CDK6, CCL2, BUB1, INHA, CDC7, PKMYT1, GSG2, PBK, BUB1B, CHEK1, LOC91461, MASTL, WEE1, AURKB, MXRA5, PKN3, VRK1, CIT, PRKCE, PLK2, MELK, PASK, TTK, NEK2, EME1, NUAK2, CDC2, CDK2, CDK4, MAP2K6, PLK1, PLK4
Mitotic chromosome condensation	6	2.73E-06	CDCA5, CNAP1, NUSAP1, HCAP-G, SMC4L1, SMC2L1
Mitosis	44	4.68E-37	KIF2C, CENPF, BUB1, SPAG5, DLG7, ACTG1, PKMYT1, CDC6, HCAP-G, MAD2L1, CCNB1, PBK, CCNF, BUB1B, ESPL1, CCNB2, WEE1, CNAP1, KIF23, SGOL1, CIT, CDC25A, TPX2, ASPM, SMC4L1, SMC2L1, MPHOSPH1, TTK, NEK2, CDC2, CDK2, CCNA2, CDC25C, PTTG1, KNTC1, KIF15, PLK1, CDCA5, CDC20, KNTC2, NUSAP1, ANLN, UBE2C, CENPE
Phosphoinositide-mediated signaling	13	8.33E-08	CKS2, RFC4, HMGB2, HIST1H4C, TYMS, SPAG5, BUB1B, TOP2A, KNTC2, ZWINT, PCNA, UBE2C, FEN1
Response to DNA damage stimulus	43	1.78E-25	RFC4, CHAF1B, FANCL, POLD3, NUDT1, UHRF1, EXO1, CHEK1, LIG1, BRCA1, TOP2A, POLE2, RAD54L, GTSE1, POLE, PCNA, RAD51, MDC1, UIP1, RAD51AP1, HMGB2, RPA1, TYMS, POLQ, NEIL3, CCNA2, CHAF1A, PTTG1, MAP2K6, RFC5, FANCG, RPA3, FANCB, XRCC3, H2AFX, TOPBP1, RECQL4, BLM, RAD51C, POLD1, FANCD2, APEX2, FEN1
Traversing start control point of mitotic cell cycle	5	2.73E-06	CDC7, CDC6, CDC2, CDK2, CDC25C
Regulation of DNA replication	5	2.14E-04	GMNN, CDC6, CDK2, CDT1, PCNA
Regulation of DNA metabolism	7	6.56E-05	BRCA1, GMNN, CDC6, CDK2, CDT1, PCNA, RAD51
Phosphate metabolism	35	1.83E-03	CDK6, CCL2, BUB1, INHA, CDC7, PKMYT1, GSG2, CDKN3, PBK, BUB1B, CHEK1, LOC91461, MASTL, WEE1, AURKB, MXRA5, PKN3, VRK1, CIT, CDC25A, PRKCE, MELK, PLK2, PASK, TTK, NEK2, EME1, NUAK2, CDC2, CDK2, CDC25C, CDK4, MAP2K6, PLK4, PLK1
Organelle organization and biogenesis	44	7.49E-08	CKS2, KRT8, PRC1, KIF2C, CENPF, SUV39H1, CHAF1B, SPAG5, EZH2, KIF14, HCAP-G, KIF4A, DIAPH3, BUB1B, ESPL1, BRCA1, ACD, HIST1H2BH, CNAP1, KIF23, CBX1, ZWINT, GTSE1, KIF11, SMC4L1, SMC2L1, EXOSC2, MPHOSPH1, STMN1, TTK, HMGB2, HIST1H4C, CENPA, KIF20A, CHAF1A, KIF15, CDCA5, H2AFX, KNTC2, MGC39900, NUSAP1, UBE2C, CENPE, C9orf48
Organelle localization	6	1.62E-06	CENPF, CDCA5, DLG7, NUSAP1, CENPE, ESPL1
Microtubule-based process	22	7.74E-11	STMN1, CKS2, PRC1, KIF2C, TTK, SPAG5, KIF14, KIF4A, KIF20A, BUB1B, ESPL1, KIF15, KNTC2, KIF23, NUSAP1, ZWINT, GTSE1, KIF11, UBE2C, CENPE, C9orf48, MPHOSPH1
Sister chromatid segregation	10	2.68E-10	CDCA5, KNTC2, CNAP1, DLG7, NUSAP1, HCAP-G, SMC4L1, CENPE, SMC2L1, ESPL1
Regulation of cyclin dependent protein kinase activity	10	1.66E-07	CHEK1, CKS2, CDK5RAP3, PKMYT1, BCCIP, CDC6, CDC25A, CDKN3, CCNA2, CDC25C
Deoxyribonucleotide biosynthesis	3	6.19E-03	RRM2, TYMS, DTYMK
Response to stress	56	1.70E-09	CCL2, EXO1, LIG1, RAD54L, BST1, GTSE1, POLE, MDK, TYMS, POLQ, NEIL3, CCNA2, PTTG1, RFC5, FANCG, RPA3, FANCB, XRCC3, H2AFX, RECQL4, HSPA2, FANCD2, APEX2, RFC4, CHAF1B, INHA, FANCL, POLD3, NUDT1, UHRF1, FOS, CHEK1, BRCA1, TOP2A, GP1BB, POLE2, PCNA, RAD51, MDC1, UIP1, RAD51AP1, FOXM1, HMGB2, RPA1, CHAF1A, MAP2K6, CFH, TOPBP1, CD14, NR3C1, BLM, CLEC2D, RAD51C, POLD1, FEN1, PRDX2
Metaphase plate congression	3	2.55E-03	CENPF, CDCA5, CENPE
Regulation of transferase activity	12	1.44E-04	CHEK1, CKS2, CDK5RAP3, TPD52L1, PKMYT1, BCCIP, CDC6, CDC25A, CDKN3, CCNA2, CDC25C, RGS4
DNA strand elongation	3	4.18E-03	PRIM1, RFC4, RFC3
Cell proliferation	37	9.94E-10	CKS2, CDK6, KIF2C, CENPF, BUB1, CDC7, SKP2, DLG7, CDC6, CDKN3, DTYMK, BUB1B, CHEK1, STIL, BRCA1, CDKN2C, CDC25A, TPX2, PCNA, IFITM1, TTK, CDK5RAP3, MDK, MKI67, CDK2, CDC25C, ADAMTS1, TSPAN3, CDK4, CDCA7, CYR61, KIF15, CDCA7L, HDGF, PLK1, E2F1, UBE2C
Establishment of organelle localization	6	4.57E-07	CENPF, CDCA5, DLG7, NUSAP1, CENPE, ESPL1
Cell organization and biogenesis	59	6.71E-06	PRC1, KIF2C, SUV39H1, DLG7, HCAP-G, DIAPH3, ESPL1, ACD, CNAP1, KIF23, CBX1, THOC4, KIF11, GTSE1, EXOSC2, MPHOSPH1, STMN1, IL17RB, CENPA, CYR61, H2AFX, KNTC2, NUSAP1, HNRPA1, C9orf48, SLC25A10, NUP107, CKS2, KRT8, CENPF, CHAF1B, SPAG5, EZH2, KIF14, KIF4A, BUB1B, BRCA1, HIST1H2BH, TRIP6, ZWINT, SMC4L1, SMC2L1, TTK, KAZALD1, HMGB2, HIST1H4C, RANBP1, IGFBP3, TMEM97, KIF20A, CHAF1A, SORT1, KIF15, PPIH, CDCA5, MGC39900, UBE2C, WISP2, CENPE
Regulation of kinase activity	12	1.35E-04	CHEK1, CKS2, CDK5RAP3, TPD52L1, PKMYT1, BCCIP, CDC6, CDC25A, CDKN3, CCNA2, CDC25C, RGS4
DNA repair	40	3.75E-24	RFC4, CHAF1B, FANCL, POLD3, NUDT1, UHRF1, EXO1, CHEK1, LIG1, BRCA1, TOP2A, POLE2, RAD54L, POLE, PCNA, RAD51, MDC1, UIP1, RAD51AP1, HMGB2, RPA1, TYMS, POLQ, NEIL3, CHAF1A, PTTG1, RFC5, FANCG, RPA3, FANCB, XRCC3, H2AFX, TOPBP1, RECQL4, BLM, RAD51C, POLD1, FANCD2, APEX2, FEN1
DNA recombination	11	3.91E-06	CHEK1, LIG1, XRCC3, H2AFX, RPA1, BLM, RAD51C, RAD54L, RAD51, RAD51AP1, EXO1
Protein complex assembly	14	7.55E-03	CENPF, HMGB2, CHAF1B, HIST1H4C, SLC7A6, MPP2, CENPA, CHAF1A, KNTC1, PPIH, H2AFX, HIST1H2BH, RAD51, CENPE
Establishment of chromosome localization	4	8.79E-05	CENPF, CDCA5, DLG7, CENPE
Chromosome segregation	15	1.42E-14	CENPF, DLG7, HCAP-G, PTTG1, SGOL2, ESPL1, CDCA5, KNTC2, CNAP1, SGOL1, NUSAP1, CDCA1, SMC4L1, SMC2L1, CENPE
Chromosome organization and biogenesis	19	9.65E-05	CENPF, SUV39H1, HMGB2, CHAF1B, HIST1H4C, EZH2, HCAP-G, CENPA, CHAF1A, CDCA5, ACD, H2AFX, CNAP1, HIST1H2BH, CBX1, NUSAP1, SMC4L1, SMC2L1, CENPE
DNA integrity checkpoint	6	2.66E-05	CHEK1, CDC6, GTSE1, CDT1, CCNA2, CDC45L
Chromosome localization	4	8.79E-05	CENPF, CDCA5, DLG7, CENPE
Spindle organization and biogenesis	11	4.01E-12	CKS2, STMN1, PRC1, TTK, KNTC2, SPAG5, KIF23, ZWINT, KIF11, UBE2C, BUB1B
Protein amino acid phosphorylation	30	8.41E-05	CDK6, CCL2, BUB1, CDC7, PKMYT1, GSG2, PBK, BUB1B, LOC91461, MASTL, CHEK1, WEE1, AURKB, MXRA5, PKN3, VRK1, CIT, PRKCE, PLK2, MELK, PASK, TTK, NEK2, NUAK2, CDC2, CDK2, CDK4, MAP2K6, PLK1, PLK4
Chromosome condensation	6	9.81E-06	CDCA5, CNAP1, NUSAP1, HCAP-G, SMC4L1, SMC2L1
Cell cycle	97	2.18E-51	PRC1, KIF2C, CDC7, GSG2, CDKN3, HCAP-G, ESPL1, LIG1, MCM5, TPD52L1, CNAP1, KIF23, RAD54L, GTSE1, STMN1, NEK2, E2F2, CDK4, SGOL2, KNTC1, PLK1, H2AFX, CKS1B, BCCIP, NUSAP1, ANLN, CKS2, CENPF, CHAF1B, ACTG1, CDC6, PBK, CHEK1, ZWINT, ASPM, RAD51, MDC1, SMC4L1, TTK, MKI67, CDK2, MCM7, KIF15, MAP2K6, CDCA5, E2F1, BIRC5, UBE2C, BUB1, PKMYT1, ILF3, DLG7, DTYMK, MAD2L1, WEE1, SGOL1, CIT, KIF11, RBL1, MPHOSPH1, MDK, CCNA2, CDT1, PTTG1, CDC45L, FANCG, PLK4, MCM3, KNTC2, GMNN, HSPA2, FANCD2, CDK6, INHA, SKP2, SPAG5, UHRF1, CCNB1, CCNF, BUB1B, CCNB2, BRCA1, CDKN2C, AURKB, TPX2, CDC25A, PCNA, SMC2L1, IFITM1, CDK5RAP3, MCM2, CDC2, CDC25C, MCM6, CHAF1A, CDC20, CENPE
Spindle checkpoint	3	4.18E-03	TTK, CENPF, BUB1
Cytoskeleton organization and biogenesis	25	4.74E-06	CKS2, KIF2C, PRC1, KRT8, SPAG5, KIF14, KIF4A, DIAPH3, BUB1B, ESPL1, KIF23, KIF11, GTSE1, ZWINT, MPHOSPH1, STMN1, TTK, KIF20A, KIF15, KNTC2, NUSAP1, MGC39900, UBE2C, C9orf48, CENPE
Chromatin assembly or disassembly	9	8.89E-03	SUV39H1, HIST1H4C, CHAF1B, HMGB2, H2AFX, HIST1H2BH, CBX1, CENPA, CHAF1A
Nucleobase, nucleoside, nucleotide and nucleic acid metabolism	121	1.16E-08	SUV39H1, Pfs2, ADARB1, ATOH8, CDC7, TAF5, CITED4, TK1, HMG1L1, EXO1, PRIM1, LIG1, MCM5, TPD52L1, ATPIF1, PAPSS2, CBX1, RAD54L, POLE, ORC6L, EXOSC2, IQGAP3, RRM2, ORC1L, TRIP13, E2F2, POLQ, ITGB3BP, CENPA, NEIL3, CHTF18, RRM1, KNTC1, RNASEH2A, ID3, RFC5, FANCB, XRCC3, H2AFX, GATA2, HNRPA1, DMBX1, NASP, RFC4, RFC2, CENPF, CHAF1B, PAICS, POLD3, CDC6, SREBF1, CHEK1, GNE, MCM4, MXD3, RAD51, MDC1, UIP1, RAD51AP1, TIMELESS, FOXM1, EME1, SLBP, HIST1H4C, CDK2, HAT1, MCM7, NR3C1, DNMT1, BLM, RAD51C, E2F1, POLD1, FEN1, ILF3, SNRPA, DTYMK, RAB26, ZNF488, THOC4, RBL1, TYMS, RPA2, CDT1, PTTG1, CDC45L, FANCG, RPA3, HOXA2, GMNN, MCM3, RECQL4, FANCD2, POLA2, APEX2, FANCL, EZH2, NUDT1, PHF19, UHRF1, FOS, POLR3K, BRCA1, TOP2A, ASCC3L1, HIST1H2BH, POLE2, PCNA, NUDT21, HMGB2, RPA1, MCM2, MCM6, CHAF1A, PPIH, SLC2A4RG, TOPBP1, RFC3, TTF2, C20orf129, CSTF3
Second-messenger-mediated signaling	16	1.53E-05	APITD1, CKS2, RFC4, GABBR2, CCL2, HMGB2, HIST1H4C, TYMS, SPAG5, BUB1B, TOP2A, KNTC2, ZWINT, PCNA, UBE2C, FEN1
Meiosis	7	4.68E-04	CHEK1, NEK2, H2AFX, SGOL1, RAD54L, HSPA2, RAD51
Regulation of protein kinase activity	12	1.35E-04	CHEK1, CKS2, CDK5RAP3, TPD52L1, PKMYT1, BCCIP, CDC6, CDC25A, CDKN3, CCNA2, CDC25C, RGS4