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Table 1 Results of pathway fragment analysis

From: Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence

Pathway fragment analysis
Pathway fragments down-regulated in both RS and SIPS
Title Number of hits Group size Expected hits P-value Adjusted P-value Hit names
 Glu ---GluR1:GluR3--- > c-fos 2 11 0.11067 0.00504 0.02521 GRIA1 (ENSG00000155511), GRIA1 (ENSG00000269977)
 GluR1:GluR2 complex 2 9 0.09055 0.00334 0.02521 GRIA1 (ENSG00000155511), GRIA1 (ENSG00000269977)
 AMPA receptor signaling 2 14 0.14086 0.00819 0.0273 GRIA1 (ENSG00000155511), GRIA1 (ENSG00000269977)
 wnt --- > beta-catenin 2 25 0.25153 0.02525 0.04864 TCF7L2, WNT2
 SDF-1 --- > G-protein 2 27 0.27165 0.02918 0.04864 CXCL12, GNG2
 SDF-1 --- > calcium mobilization 2 26 0.26159 0.02718 0.04864 CXCL12, GNG2
Pathway fragments up-regulated in both RS and SIPS
 Caspase-3 ---/ K18 2 3 0.04856 7.5719E-4 0.00909 CASP3, KRT18
 Aurora-A(h) ---/ p53(h) 2 3 0.04856 7.5719E-4 0.00909 AURKA, MDM2
 glutamate metabolism 3 16 0.25897 0.00189 0.01513 ABAT, GCLM, GLS
 L-glutamate ---ammonia--- > 2-oxoglutarate 2 8 0.12948 0.00671 0.01611 ABAT, GLS
 xanthosine-5-phosphate --- > allantoin 2 8 0.12948 0.00671 0.01611 NT5E, PNP
 IMP --- > xanthine 2 8 0.12948 0.00671 0.01611 NT5E, PNP
 dGDP --- > guanine 2 7 0.1133 0.00509 0.01611 NT5E, PNP
 dADP --- > hypoxanthine 2 7 0.1133 0.00509 0.01611 NT5E, PNP
 L-ornithine --- > succinate 2 8 0.12948 0.00671 0.01611 ABAT, ODC1
 polyamine metabolism 2 8 0.12948 0.00671 0.01611 ABAT, ODC1
 plasmenylethanolamine --- > plasmenylcholine 2 10 0.16185 0.01057 0.02307 EPT1, PLCB4
 GDP --- > xanthine 2 12 0.19423 0.01519 0.03039 NT5E, PNP
 interconversions and degradations of purine ribonucleotides 3 41 0.6636 0.02728 0.04365 AMPD3, NT5E, PNP
 L-tryptophan --- > NAD+, NADPH 2 16 0.25897 0.02653 0.04365 NAMPT, NMNAT2
 biosynthesis and degradation of nicotinamide,NAD+,NADP+ 2 16 0.25897 0.02653 0.04365 NAMPT, NMNAT2
 plasmenylcholine biosynthesis 2 19 0.30752 0.03667 0.05501 EPT1, PLCB4
Pathway fragments down-regulated in RS
 acetyl-CoA, acetoacetyl-CoA --- > cholesterol, fatty acid 7 21 0.90945 1.6325E-5 5.7683E-4 FDFT1, FDPS, HMGCS1, IDI1, LSS, MVD, SQLE
 cholesterol metabolism 7 21 0.90945 1.6325E-5 5.7683E-4 FDFT1, FDPS, HMGCS1, IDI1, LSS, MVD, SQLE
 biosynthesis of saturated and n - 9 series of MUFA and PUFA 5 9 0.38976 1.5131E-5 5.7683E-4 ELOVL6, FADS1, FADS2, FASN, SCD
 17-alpha-hydroxyprogesterone --- > 5alpha-androstanediol 3 5 0.21654 7.3989E-4 0.01569 AKR1C1 (ENSG00000187134), AKR1C2 (ENSG00000151632), SRD5A3
 acetyl-CoA, malonyl-CoA --- > lignoceric acid 3 5 0.21654 7.3989E-4 0.01569 ELOVL6, FADS2, FASN
 HMGCR regulation 9 65 2.81496 0.00158 0.02785 EGFR, FDFT1, FDPS, HMGCS1, IDI1, INSIG1, LSS, MVD, SQLE
Pathway fragments up-regulated in RS
 Aurora-B cell cycle regulation 17 55 4.09011 1.676E-7 4.0727E-5 BIRC5, BUB1, BUB1B, CCNB1, CCNB2, CDC20, CDCA8, CDK1, CENPE, CUL1, INCENP, MAD2L1, PLK1, TTK, UBB, UBE2C, ZC3HC1
 Cdk1, Plk1 ---/ cyclin B 5 5 0.37183 2.1527E-6 1.7437E-4 CCNB1, CDC20, CDK1, CKS1B, PLK1
 Plk1 --- > Bub1 5 5 0.37183 2.1527E-6 1.7437E-4 BUB1, CCNB1, CCNB2, CDK1, PLK1
 Plk1 --- > INCENP 5 6 0.44619 1.2138E-5 7.3737E-4 CCNB1, CCNB2, CDK1, INCENP, PLK1
 Plk1 activation and substrates 9 24 1.78478 2.7847E-5 0.00135 BRCA2, CCNB1, CCNB2, CDK1, KIF23, PLK1, PRKACB, RAD51, STK10
 CENP-E --- > BubR1 5 7 0.52056 3.9925E-5 0.00162 BUB1, BUB1B, CENPE, MAD2L1, TTK
 cyclosome regulation 16 75 5.57743 7.6369E-5 0.00265 CCNA2, CCNB1, CCNB2, CDC20, CDK1, CKS1B, CUL1, FBXO5, MAD2L1, NDC80, PLK1, SKP2, UBB, UBE2C, UBE2E2, UBE2S
 cyclosome regulatory network 16 77 5.72616 1.0692E-4 0.00289 CCNA2, CCNB1, CCNB2, CDC20, CDK1, CKS1B, CUL1, FBXO5, MAD2L1, NDC80, PLK1, SKP2, UBB, UBE2C, UBE2E2, UBE2S
 Cdc20 ubiquitination 8 22 1.63605 1.03E-4 0.00289 BUB1B, CCNB1, CDC20, CDK1, CKS1B, MAD2L1, UBB, UBE2C
 Cdc20 deubiquitination 8 23 1.71041 1.4802E-4 0.0036 BUB1B, CCNB1, CDC20, CDK1, CKS1B, MAD2L1, UBB, UBE2C
 Plk1 cell cycle regulation 12 52 3.86702 2.8909E-4 0.00585 BRCA2, CCNB1, CCNB2, CDK1, CUL1, FBXO5, KIF23, PLK1, PRKACB, RAD51, STK10, UBB
 Metaphase to Anaphase transition 12 52 3.86702 2.8909E-4 0.00585 BUB1, BUB1B, CCNB1, CDC20, CDK1, CKS1B, FBXO5, MAD2L1, NEK2, PLK1, UBB, UBE2C
 Bub1 --- > APC7 4 6 0.44619 3.9379E-4 0.00736 BUB1, BUB1B, CDC20, MAD2L1
 S phase (Cdk2) 12 55 4.09011 5.0416E-4 0.00875 CCNA2, CDK1, CDKN3, CKS1B, CUL1, E2F3, E2F8, PPM1A, PPM1B, PPM1D, SKP2, UBB
 ID complex deubiquitylation 4 7 0.52056 8.6562E-4 0.01402 CDK1, FANCD2, FANCI, UBB
 borealin --- > Aurora-B 3 4 0.29746 0.00153 0.02323 BIRC5, CDCA8, INCENP
 Pin1 --- > APP 3 5 0.37183 0.00361 0.05167 CCNB1, CCNB2, CDK1
Pathway fragments down-regulated in SIPS
No significant findings
Pathway fragments up-regulated in SIPS
 HMGCR regulation 21 65 6.1986 1.9691E-7 6.4979E-5 CAB39, CAB39L, CYP51A1, DHCR7, EGFR, FDFT1, FDPS, HMGCS1, IDI1, LIPA, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, SC5D, TM7SF2, UFD1L, VCP
 acetyl-CoA, acetoacetyl-CoA --- > cholesterol, fatty acid 9 21 2.00262 5.8742E-5 0.00646 CYP51A1, DHCR7, FDFT1, FDPS, HMGCS1, IDI1, LIPA, SC5D, TM7SF2
 cholesterol metabolism 9 21 2.00262 5.8742E-5 0.00646 CYP51A1, DHCR7, FDFT1, FDPS, HMGCS1, IDI1, LIPA, SC5D, TM7SF2
 parkin associated pathways 15 65 6.1986 8.2044E-4 0.03437 CALM2, DNAJA1, HSPA8, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, TUBA1C, TUBB6, UBE2G1, UBE2L3, UBE2N
 Mdm2 --- > p/CAF 8 23 2.19335 8.3317E-4 0.03437 PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, TAF9 (ENSG00000085231)
 HMGCR --- > 26S proteasome 9 28 2.67017 7.5931E-4 0.03437 PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, UFD1L, VCP
 ER-alpha ---CHIP--- > 26S proteasome 9 28 2.67017 7.5931E-4 0.03437 HSP90AA1, HSPA8, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8
 cofilin-1 degradation 8 22 2.09799 5.9124E-4 0.03437 CFL1, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8
 Smac ---/ cIAP-2 8 24 2.28871 0.00115 0.03446 BIRC3, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8
 E1 ---/ alpha-synuclein 8 24 2.28871 0.00115 0.03446 PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, UBE2L3
 NIK degradation 8 24 2.28871 0.00115 0.03446 PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, TRAF3
 Caspase network 17 82 7.81977 0.00137 0.03759 BID, BIRC3, CDC42, CFLAR, CRADD, DFFA, HSPD1, MCL1, PSMA7, PSMC1, PSMC4, PSMC5, PSMD11, PSMD2, PSMD8, UBE2L3, XIAP