Table 3 Overlapping in vivo and in vitro DEGs and selected IPEC-J2 effector genes from ZnO, rye and amoxicillin datasets
Gene symbol | Full name | Day in vivo/hours in vitro IPEC-J2 | Function/part of process |
|---|---|---|---|
ZnO overlapping genes | |||
ZFP36L2 | ZFP36 ring finger protein-like 2 | 23 days/2 h | Promotion mRNAs deadenylation and degradation |
MT1A | Metallothionein 1A | 23 and 35 days-ileum-23 days-jej/2 and 6 h | Divalent metal ion transporter and scavenger of oxygen radicals |
ZnO; putative IPEC-J2 effector genes | Related or overlapping in vivo pathway | ||
HBEGF | HBEGF (heparin-binding EGF-like growth factor) | PAK pathway | Mitogenic for fibroblasts multiple organ systems |
NRG1 | NRG1 (neuregulin 1) | PAK pathway | Growth and development of multiple organ systems |
BMP2 | BMP2 (bone morphogenetic protein 2) | PAK pathway | Member TGF-beta superfamily/induces bone and cartilage formation |
NGF | Nerve growth factor | PAK pathway | Nerve growth-stimulating activity |
MT1A | MT1A (metallothionein 1A) | Mineral absorption | Divalent metal ion transporter and scavenger of oxygen radicals |
HMOX1 | Heme oxygenase 1 | Mineral absorption | Enzyme heme catabolism/response to hypoxya/Fe2+ transport/regulation of vascular tone |
SERPINE1 | SERPINE1 (serpin family E member 1) | Cell adhesion_ECM remodelling | Serine protease inhibitor/inhibitor of fibrinolysis |
IL6 | Interleukin 6 | Influenza A/PAK pathway | Cytokine that induces inflammation and maturation of B cells |
IFNL1 | Interferon λ1 | Influenza A/PAK pathway | Antiviral host defence in the epithelial tissues |
IL1A | Interleukin 1A | Influenza A/PAK pathway | Pleiotropic cytokine/role in various immune responses and inflammation/antiviral response |
IL8 | (Interleukin 8) | Influenza A/PAK pathway | Chemotactic factor attracting neutrophils, basophils, and T cells |
IL21 | (Interleukin 21) | None | Cytokine promoting switch between innate and adaptive immunity |
Rye overlapping genes | |||
HOOK3 | Hook microtubule-tethering protein 3 | 10% 21 days, 10 vs. 5% 28 days, 10% 28 days/2 h | Component FTS/Hook/FHIP complex/vesicle trafficking |
PTEN | Phosphatase and tensin Homolog | 10% 21 days, 10 vs. 5% 28 days, 10% 28 days/2 h | Protein tyrosine Phosphatases/negatively regulating AKT-PKB signalling |
ZFYVE16 | Zinc finger, FYVE domain-containing 16 | 10% 21 days, 10 vs. 5% 28d/2 h | Recruits TGF transcriptional modulators/membrane trafficking endosomes |
CCK | Cholecystokinin | 10% 21 days, 10 vs. 5% 28d/2 h | Peptide hormone induces release of pancreatic enzymes |
NOG | Noggin | 5% 21 days/2 h | Inactivates members of TGF-beta family signalling proteins (e.g BMPs) |
MUC(17) | Mucin 17, cell surface-associated | 5%-21d, 10% vs. 5% 21d/6 h | Membrane-bound mucin that provides protection to gut epithelial cells |
Rye; putative IPEC-J2 effector genes | Related or overlapping in vivo pathway | ||
TNF | Tumour necrosis factor | TGF-beta signalling | Multifunctional proinflammatory cytokine |
FST | Follistatin (activin-binding protein) | TGF-beta signalling | Inhibits follicle-stimulating hormone release/antagonist of INHBA |
RICTOR | RPTOR independent companion of MTOR complex 2 | mTOR signalling | Subunit of mTORC2/regulates cell growth and survival in response to hormones |
DDIT4 | DNA damage-inducible transcript 4 | mTOR signalling | Regulation cell growth and survival/inhibition activity mTORC1 in response of hypoxia |
MUC(4) | Mucin 4, cell surface-associated | N- and O-linked glycan synthesis | Sialomucin/intestinal epithelial cell differentiation/EGF cell signalling |
MUC(13) | Mucin 13, cell surface Associated | N- and O-linked glycan synthesis | Epithelial and hemopoietic transmembrane mucin/EGF cell signalling |
B3GALT1 | Beta-1,3-galactosyltransferase 1 | N- and O-linked glycan synthesis | Transfers galactose from UDP galactose to a terminal beta-N-acetylglucosamine |
Amoxicillin-overlapping genes | |||
OSER1 | Oxidative stress responsive serine-rich 1 | 5/2 h | Cellular response to hydrogen peroxide/UBC binding |
ZBTB17 | Zinc finger and BTB domain-containing 17 | 5/6 h | c-MYC transcriptional repression (regulation of cell cyle) |
MID1IP1 | MID1-interacting protein 1 | 5/6 h | Negative regulation of microtubule (de)polymerisation/UBC binding |
STMN1 | Stathmin 1a | 5 and 14/ | Prevents assembly and promotes disassembly of microtubules/UBC binding |
EREG | Epiregulina | 5 and 14/ | Member of the epidermal growth factor family/UBC binding |
CLTA | Clathrin, light chain Aa | 5 and 14/ | Coated pits and vesicles and receptor-mediated endocytosis/UBC binding |
ARPC1A | Actin-related protein 2/3 complex, subunit 1Aa | 5 and 14/ | Actin polymerisation-forming of filopodia or stress fibres/UBC binding |
Amoxicillin; putative IPEC-J2 effector genes | Related or overlapping in vivo pathway | ||
HMOX1 | Heme oxygenase 1 | HIF1A pathway | Essential enzyme heme catabolism/response to hypoxia/regulation of vascular tone |
HK2 | Hexokinase 2 | HIF1A pathway | Phosphorylate glucose to produce glucose-6-phosphate |
PDK1 | Pyruvate dehydrogenase kinase 1 | HIF1A pathway | Regulation of glucose and fatty acid metabolism/upregulated in response to hypoxia |
EDN1 | Endothelin 1 | HIF1A pathway | Potent vasoconstrictor |
NPPA | Natriuretic peptide A | HIF1A pathway | Regulation blood pressure and body fluid homeostasis |
MID1 | Midline 1 RING finger protein | Microtubule | E3 ubiquitin ligase/microtubule (de)polymerisation/UBC binding |