Table 4.
Genes regulated by tretinoin in rumen papillae tissue
| Symbol | Entrez gene name | Fold change1 | FDR2 | Location | Type(s) |
|---|---|---|---|---|---|
| SFTPC | Surfactant protein C | 15.731 | 6.95E-05 | Extracellular space | Other |
| CDKN2A | Cyclin-dependent kinase inhibitor 2A | 14.833 | 3.44E-04 | Nucleus | Transcription regulator |
| MSLN | Mesothelin | 14.337 | 5.37E-03 | Extracellular space | Other |
| CYP4F2 | Cytochrome P450, family 4, subfamily F, polypeptide 2 | 14.255 | 5.63E-17 | Cytoplasm | Enzyme |
| NEU4 | Sialidase 4 | 7.214 | 1.56E-03 | Cytoplasm | Enzyme |
| SLC27A2 | Solute carrier family 27 (fatty acid transporter), member 2 | 7.161 | 2.84E-15 | Cytoplasm | Transporter |
| SIX1 | SIX homeobox 1 | 6.675 | 1.69E-04 | Nucleus | Transcription regulator |
| TNC | Tenascin C | 6.034 | 8.28E-04 | Extracellular space | Other |
| CES1 | Carboxylesterase 1 | 5.812 | 3.44E-04 | Cytoplasm | Enzyme |
| CYP1A1 | Cytochrome P450, family 1, subfamily A, polypeptide 1 | 5.111 | 4.60E-03 | Cytoplasm | Enzyme |
| SLA | Src-like-adaptor | 3.589 | 9.81E-05 | Plasma membrane | Other |
| AREG | Amphiregulin | 3.566 | 1.95E-03 | Extracellular space | Growth factor |
| A2M | α-2-macroglobulin | 3.543 | 5.08E-03 | Extracellular space | Transporter |
| DUSP4 | Dual specificity phosphatase 4 | 3.494 | 4.82E-03 | Nucleus | Phosphatase |
| EBI3 | Epstein-Barr virus induced 3 | 3.48 | 6.85E-04 | Extracellular space | Cytokine |
| BMP6 | Bone morphogenetic protein 6 | 3.453 | 6.37E-05 | Extracellular space | Growth factor |
| ALDH1A2 | Aldehyde dehydrogenase 1 family, member A2 | 3.445 | 7.74E-03 | Cytoplasm | Enzyme |
| CCR1 | Chemokine (C-C motif) receptor 1 | 3.425 | 1.12E-03 | Plasma membrane | G-protein coupled receptor |
| ALDH1A3 | Aldehyde dehydrogenase 1 family, member A3 | 3.274 | 2.77E-03 | Cytoplasm | Enzyme |
| PLEK | Pleckstrin | 3.273 | 1.37E-02 | Cytoplasm | Other |
| ALPL | Alkaline phosphatase, liver/bone/kidney | 3.185 | 8.35E-05 | Plasma membrane | Phosphatase |
| CCR5 | Chemokine (C-C motif) receptor 5 (gene/pseudogene) | 3.121 | 7.27E-03 | Plasma membrane | G-protein coupled receptor |
| CTGF | Connective tissue growth factor | 3.116 | 1.03E-02 | Extracellular space | Growth factor |
| TLR5 | Toll-like receptor 5 | 3.1 | 2.96E-03 | Plasma membrane | Transmembrane receptor |
| PTPN22 | Protein tyrosine phosphatase, non-receptor type 22 (lymphoid) | 2.883 | 1.53E-02 | Cytoplasm | Phosphatase |
| THBS1 | Thrombospondin 1 | 2.851 | 1.03E-02 | Extracellular space | Other |
| NOV | Nephroblastoma overexpressed | 2.818 | 4.67E-02 | Extracellular space | Growth factor |
| ANPEP | Alanyl (membrane) aminopeptidase | 2.817 | 2.10E-02 | Plasma membrane | Peptidase |
| SCML1 | Sex comb on midleg-like 1 (Drosophila) | 2.814 | 5.60E-03 | Nucleus | Transcription regulator |
| SOAT1 | Sterol O-acyltransferase 1 | 2.774 | 1.47E-07 | Cytoplasm | Enzyme |
| MMP28 | Matrix metallopeptidase 28 | 2.76 | 1.13E-09 | Extracellular space | Peptidase |
| CTSL | Cathepsin L | 2.678 | 2.61E-02 | Cytoplasm | Peptidase |
| C1QA | Complement component 1, q subcomponent, A chain | 2.625 | 7.58E-03 | Extracellular space | Other |
| VSIG4 | V-set and immunoglobulin domain containing 4 | 2.623 | 2.56E-02 | Plasma membrane | Other |
| AMICA1 | Adhesion molecule, interacts with CXADR antigen 1 | 2.523 | 7.94E-06 | Plasma membrane | Other |
| CD52 | CD52 molecule | 2.522 | 5.02E-03 | Plasma membrane | Other |
| CD101 | CD101 molecule | 2.504 | 4.32E-03 | Plasma membrane | Other |
| FABP4 | Fatty acid binding protein 4, adipocyte | 2.496 | 3.53E-03 | Cytoplasm | Transporter |
| HMGCS2 | 3-Hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) | 2.491 | 4.20E-05 | Cytoplasm | Enzyme |
| IGFBP5 | Insulin-like growth factor binding protein 5 | 2.452 | 9.78E-04 | Extracellular space | Other |
| CD86 | CD86 molecule | 2.404 | 5.74E-03 | Plasma membrane | Transmembrane receptor |
| RBP2 | Retinol binding protein 2, cellular | 2.401 | 2.18E-03 | Cytoplasm | Transporter |
| APOA2 | Apolipoprotein A-II | 2.389 | 7.94E-06 | Extracellular space | Transporter |
| SEMA7A | Semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group) | 2.374 | 1.44E-02 | Plasma membrane | Transmembrane receptor |
| BAMBI | BMP and activin membrane-bound inhibitor | 2.374 | 2.89E-03 | Plasma membrane | Other |
| GGT1 | γ-Glutamyltransferase 1 | 2.365 | 2.67E-02 | Plasma membrane | Enzyme |
| POMC | Proopiomelanocortin | 2.343 | 1.19E-04 | Extracellular space | Other |
| CD68 | CD68 molecule | 2.337 | 4.21E-03 | Plasma membrane | Other |
| CD38 | CD38 molecule | 2.332 | 3.81E-02 | Plasma membrane | Enzyme |
| SLAMF7 | SLAM family member 7 | 2.316 | 2.30E-02 | Plasma membrane | Other |
| CYP4F3 | Cytochrome P450, family 4, subfamily F, polypeptide 3 | 2.302 | 1.12E-03 | Cytoplasm | Enzyme |
| ECI2 | Enoyl-CoA delta isomerase 2 | 2.289 | 2.31E-05 | Cytoplasm | Enzyme |
| TYROBP | TYRO protein tyrosine kinase binding protein | 2.288 | 2.73E-03 | Plasma membrane | Transmembrane receptor |
| RGS5 | Regulator of G-protein signaling 5 | 2.276 | 4.61E-02 | Plasma membrane | Other |
| ITGB2 | Integrin, β 2 (complement component 3 receptor 3 and 4 subunit) | 2.253 | 3.60E-04 | Plasma membrane | Transmembrane receptor |
| ITGAM | Integrin, α M (complement component 3 receptor 3 subunit) | 2.245 | 2.53E-02 | Plasma membrane | Transmembrane receptor |
| MGST3 | Microsomal glutathione S-transferase 3 | 2.237 | 2.79E-05 | Cytoplasm | Enzyme |
| BNIP3L | BCL2/adenovirus E1B 19kDa interacting protein 3-like | 2.231 | 2.39E-06 | Cytoplasm | Other |
| HLA-DMB | Major histocompatibility complex, class II, DM beta | 2.207 | 1.58E-04 | Plasma membrane | Transmembrane receptor |
| FOLR2 | Folate receptor 2 (fetal) | 2.206 | 1.12E-02 | Plasma membrane | Transporter |
| MFNG | MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase | 2.177 | 1.38E-02 | Cytoplasm | Enzyme |
| SPI1 | Spi-1 proto-oncogene | 2.172 | 4.23E-03 | Nucleus | Transcription regulator |
| IKZF1 | IKAROS family zinc finger 1 (Ikaros) | 2.165 | 8.46E-03 | Nucleus | Transcription regulator |
| CFP | Complement factor properdin | 2.165 | 7.82E-03 | Extracellular space | Other |
| CXCR4 | Chemokine (C-X-C motif) receptor 4 | 2.09 | 9.76E-03 | Plasma membrane | G-protein coupled receptor |
| CIDEA | Cell death-inducing DFFA-like effector a | 2.085 | 3.59E-02 | Cytoplasm | Other |
| RPL6 | Ribosomal protein L6 | 2.055 | 1.27E-02 | Cytoplasm | Other |
| COL4A1 | Collagen, type IV, alpha 1 | 2.024 | 1.40E-03 | Extracellular space | Other |
| TNFRSF1B | Tumor necrosis factor receptor superfamily, member 1B | 2.009 | 3.27E-04 | Plasma membrane | Transmembrane receptor |
| MAOB | Monoamine oxidase B | 2.002 | 7.89E-03 | Cytoplasm | Enzyme |
| KLF9 | Kruppel-like factor 9 | −2.011 | 1.35E-04 | Nucleus | Transcription regulator |
| BTC | betacellulin | −2.042 | 2.68E-02 | Extracellular space | Growth factor |
| MYBL2 | v-myb avian myeloblastosis viral oncogene homolog- like 2 | −2.109 | 2.85E-02 | Nucleus | Transcription regulator |
| TSC22D3 | TSC22 domain family, member 3 | −2.116 | 1.31E-04 | Nucleus | Transcription regulator |
| SOX6 | SRY (sex determining region Y)-box 6 | −2.129 | 2.14E-02 | Nucleus | Transcription regulator |
| DLL1 | δ-Like 1 (Drosophila) | −2.154 | 1.79E-03 | Plasma membrane | Enzyme |
| KRT15 | Keratin 15 | −2.166 | 1.11E-03 | Cytoplasm | Other |
| HES1 | Hes family bHLH transcription factor 1 | −2.169 | 6.79E-03 | Nucleus | Transcription regulator |
| CEACAM1 | Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) | −2.172 | 1.12E-02 | Plasma membrane | Other |
| KIF23 | Kinesin family member 23 | −2.181 | 2.57E-03 | Cytoplasm | Other |
| HOXD4 | Homeobox D4 | −2.212 | 1.81E-02 | Nucleus | Transcription regulator |
| HEY1 | Hes-related family bHLH transcription factor with YRPW motif 1 | −2.22 | 1.12E-02 | Nucleus | Transcription regulator |
| DUSP1 | Dual specificity phosphatase 1 | −2.259 | 3.10E-02 | Nucleus | Phosphatase |
| MYB | v-myb avian myeloblastosis viral oncogene homolog | −2.285 | 1.84E-02 | Nucleus | Transcription regulator |
| PTCH1 | Patched 1 | −2.319 | 3.84E-03 | Plasma membrane | Transmembrane receptor |
| IGFBP3 | Insulin-like growth factor binding protein 3 | −2.437 | 7.34E-03 | Extracellular space | Other |
| IGF2 | Insulin-like growth factor 2 | −2.472 | 3.57E-05 | Extracellular space | Growth factor |
| FGF2 | Fibroblast growth factor 2 (basic) | −2.476 | 2.82E-02 | Extracellular space | Growth factor |
| COL4A5 | Collagen, type IV, alpha 5 | −2.481 | 4.70E-03 | Extracellular space | Other |
| ITGA2 | Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) | −2.507 | 6.26E-05 | Plasma membrane | Transmembrane receptor |
| GJB5 | Gap junction protein, beta 5, 31.1kDa | −2.615 | 7.49E-03 | Plasma membrane | Transporter |
| IGFBP2 | Insulin-like growth factor binding protein 2, 36kDa | −2.711 | 1.65E-03 | Extracellular space | Other |
| IGFBP6 | Insulin-like growth factor binding protein 6 | −2.797 | 1.94E-03 | Extracellular space | Other |
| STC1 | Stanniocalcin 1 | −2.923 | 5.90E-03 | Extracellular space | Kinase |
| F3 | Coagulation factor III (thromboplastin, tissue factor) | −2.96 | 1.87E-04 | Plasma membrane | Transmembrane receptor |
| HS3ST1 | Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 | −3.044 | 6.26E-05 | Cytoplasm | Enzyme |
| RNASE1 | Ribonuclease, RNase A family, 1 (pancreatic) | −3.056 | 2.31E-02 | Extracellular space | Enzyme |
| GATA6 | GATA binding protein 6 | −3.173 | 1.12E-02 | Nucleus | Transcription regulator |
| TERT | Telomerase reverse transcriptase | −3.239 | 3.14E-03 | Nucleus | Enzyme |
| GHR | Growth hormone receptor | −3.268 | 2.20E-05 | Plasma membrane | Transmembrane receptor |
| CHL1 | Cell adhesion molecule L1-like | −3.721 | 1.88E-02 | Plasma membrane | Other |
| SYCP3 | Synaptonemal complex protein 3 | −4.417 | 2.38E-05 | Nucleus | Other |
| SLC12A2 | Solute carrier family 12 (sodium/potassium/chloride transporter), member 2 | −4.847 | 3.85E-07 | Plasma membrane | Transporter |
| CFTR | Cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) | −4.953 | 1.01E-06 | Plasma membrane | Ion channel |
| OAS2 | 2ʹ-5ʹ-Oligoadenylate synthetase 2, 69/71kDa | −5.376 | 7.18E-05 | Cytoplasm | Enzyme |
| BMPR1B | Bone morphogenetic protein receptor, type IB | −6.669 | 2.95E-03 | Plasma membrane | Kinase |
| PITX2 | Paired-like homeodomain 2 | −7.073 | 3.43E-02 | Nucleus | Transcription regulator |
| RXRG | Retinoid X receptor, gamma | −7.723 | 2.15E-02 | Nucleus | Ligand-dependent nuclear receptor |
| NTRK2 | Neurotrophic tyrosine kinase, receptor, type 2 | −8.077 | 1.09E-09 | Plasma membrane | Kinase |
| HOXB9 | Homeobox B9 | −8.378 | 4.76E-02 | Nucleus | Transcription regulator |
| DSG1 | Desmoglein 1 | −9.067 | 3.88E-09 | Plasma membrane | Other |
| EYA2 | EYA transcriptional coactivator and phosphatase 2 | −19.365 | 2.07E-05 | Nucleus | Phosphatase |
1Fold change: Values indicate the relative gene expression. Positive values indicate higher expression in weaned than in suckling calves, and negative values indicate the opposite.
2FDR = false discovery rate.