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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