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Table 1 Genes from each cluster assembled in networks and their top functions/canonical pathways. Gene names in bold are "focus genes" identified as VHV and served to identify key elements in hypothetical networks constructed by IPA. Statistically significant top functions and canonical pathways are identified by IPA. Hypothetical networks identified by IPA as being potentially present were pruned to remove genes that were not identified as being expressed.

From: Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis

Cluster Gene names Network's top functions Canonical pathways
#1 0.5 hours post infection, up ACTR2 , C12orf23 , CGI-38 , CPM , DGKE , FLJ22471 , GALNT10 , H2AFY2 , LOC197350 , LRRC51 , MAD1L1 , PHOSPHO2 , PIP5K1A , PPIB , PTCRA , PTPRN2 , TEKT1 , TMTC4, *,* No significant networks assembled Cell Cycle, Cell Death, Cell-to Cell Signaling and Interaction, Immune and Lymphatic System Development and Function O-glycan biosynthesis, Phospholipid Degradation, Inositol Phosphate Metabolism, Glycerophospholipid Metabolism, Glycerolipid Metabolism
#2 1 hours post infection, up ACP1, AKT2, BBC3, CD19, CHGA, CKM, CSDA, CTSD, DDX5, EEF2, EGR1, GTF2I, HAS2, HOXA5, IER3, IGF1, MYC, PGK1, PRDM1, PRNP, ROCK2, RPS6, SRC, TLN1 Cellular Growth and Proliferation, Cellular Development, Cell Death, Cell-to-Cell Signaling and Interaction, Tissue Development Neuregulin Signaling, Ephrin Receptor Signaling, Wnt/β-catenin Signaling, PDGF Signaling, Integrin Signaling, ERK/MAPK Signaling, B Cell Receptor Signaling
#3 1.5 hours post infection, up ADK, APBB1, BTN3A3, CHST2, CLIC1, EB-1, EI24, ENAH, F2, FARS2 , FAS, FOS, GNPAT , GRB7 , IL2RA , KAL1 , NDRG1, PDRG1, PRKAB2, SMARCB1, TCF3, TNF, TP53, TP73L, TWIST2, VASP Cellular Movement, Organismal Survival, Connective Tissue Development and Function, Cell Cycle Apoptosis signaling, Wnt/β-catenin Signaling, PPAR Signaling, p38 MAPK Signaling, Integrin Signaling, IL-6,-2,-10 Signaling, Death Receptor Signaling
#4 1.5 hours post infection, down AATF, AKT3, ARNTL , CENPF , COL18A1, CREG1, CRI1, CTDSPL, E2F1, E4F1, EP300, FEZ1, HIF1AN, KCNJ1, KLF5, POLR2F , PPT2, PRKCZ, RB1, RBBP9, SLC29A2, SRC, STAT5B, TBP, UMPS, ZBTB16 Cellular Growth and Proliferation, Gene Expression, Cellular Development, Cell Death, Cell Cycle Estrogen Receptor Signaling, NF-κB Signaling, Neuregulin Signaling, Xenobiotic Metabolism Signaling, Wnt/β-catenin Signaling, Pyrimidine Metabolism, PTEN Signaling, PPAR Signaling, Jak/Stat Signaling, Integrin Signaling, IL-2 Signaling
#5 4 hours post infection, up ABCA1, ALPP, C7, CCNG2, ENPP1, ERBB3, F3, FLOT1, FPRL1, G6PD, IL1B, KLF10, KRT17, MEFV, NAB2, PCSK1, PTX3 , RRS1, S100A6, SERPINH1, SLC20A1, TGFB1, THBD, TNFAIP2 Cellular Growth and Proliferation, Hematological Disease, Cellular Movement, Organismal Development, Cell-to Cell Signaling and Interaction Complement and Coagulation Cascades, p38 MAPK Signaling, Xenobiotic Metabolism Signaling, Wnt/β-catenin Signaling, TGF-β Signaling, Starch and Sucrose Metabolism, Riboflavin Metabolism, Purine Metabolism, PPAR Signaling
#6 4 hours post infection, down ARL3, CASP14, FCER1A, FOXC1, G0S2, HOXA9, KIF3C, KPNA3,MLL, NDUFS4, NDUFV2 , PEX14 , RANBP9 , RBL1, RFP, SERPINB10, SERPINC1 , SERPINE1 , SLC34A1, SLC7A1, SMYD3, TFE3, TGFB1, TNF, WWOX Cellular Development, Cellular Growth and Proliferation, Hematological System Development and Function, Immune and Lymphatic System Development and Function Ubiquinone Biosynthesis, TGF-β Signaling, p38 MAPK Signaling, Oxidative Phosphorylation, Complement and Coagulation Cascades, Cell Cycle G1/S Checkpoint Regulation, Xenobiotic Metabolism Signaling, Wnt/β-catenin Signaling, PPAR Signaling
#7 6 hours post infection, up P29 , CIRH1A , KIF1B , GPR51 , GPS1 , BMPR2 , THBD*,* No significant networks assembled Cell Morphology, Cardiovascular Disease, Genetic Disorder, Nervous System Development and Function, Organ Morphology Pentose Phosphate Pathway, EGF Signaling, IL-2 Signaling, Jak/Stat Signaling, Fructose and Mannose Metabolism, Galactose Metabolism
#8 8 hours post infection, up CCR2, CDC45L, CRABP2, CSF3R, DIO1, E2F1, EXOSC9, GBP2, IL4, IL6, INDO, KCNJ5, KIAA0101, MAZ, NR1H4 , NUP62 , PFKL, POLD1, PROS1, RAF1, RXRA, SP1, THRA Gene Expression, Cell Death, Hepatic System Disease, Cellular Function and Maintenance, Cellular Growth and Proliferation Xenobiotic Metabolism Signaling, IL-10,-6 Signaling, PPAR Signaling, VEGF Signaling, Tryptophan Metabolism, TGF-β Signaling, T Cell Receptor Signaling, Pyrimidine Metabolism
#9 8 hours post infection, down ALAD, CPT2, CPT1A, CRYAB, EEF2, GAS1, GCK, GSK3A, INSR, MNT, MXI1, MYC, NDRG1, ONECUT1, PDE3B, PKLR, PTPN2, PTPRG, RPL5, SOCS6, SORBS1, TAT, TUB Metabolic Disease, Cell Cycle, Connective Tissue Development and Function, Cellular Growth and Proliferation, Carbohydrate Metabolism Insulin Receptor Signaling, Wnt/β-catenin Signaling, Purine Metabolism, Glycolysis/Glyconeogenesis, Fatty Acid Metabolism, Tyrosine Metabolism
#10 10 hours post infection, down ACTN4, ADAM10, AIM1, ARID1B, COL2A1, CTNNB1, CTNNBIP1, CTSH, FZD8, IHH, LFNG, MMP2, NOTCH1, NRP2, PIN1, SFTPB, SLC26A2, SMARCA4, SOCS1, STXBP3 Organismal Development, Embryonic Development, Tissue Development, Cellular Development Wnt/β-catenin Signaling, NOTCH Signaling, VEGF Signaling, Purine Metabolism, PI3K/AKT Signaling, Jak/Stat Signaling, Interferon Signaling, Integrin Signaling, IL-6,-4,-2 Signaling