Table 1 Significant functional categories based on genes commonly regulated by TNT in vivo and in vitro
From: In vitro gene regulatory networks predict in vivo function of liver
Category | P-value | Downregulated genes* | Upregulated genes* |
|---|---|---|---|
Cell Cycle | 5.1E-07-1E-02 | ANGPTL2, LGALS1, CYP26B1, COL1A1, CCND2, CKAP2, CDKN3, KIF20A, CXCL12, ECT2, CCNB1, RARB, PTTG1, LZTS1, TFDP2, BCL2A1, CDC2, INPP5D | MYC, CCNC, DNM1L, NRG2(includesEG:9542), MAPK1, NRG1, TFRC, PPARG, CREG1, RIOK3, NTRK1, DUSP13, ADM |
Carbohydrate Metabolism | 1.36E-06-1E-02 | GCK, MMP2, INPP5 D, PTTG1, CXCL12, LGALS1 | NQO1, ADM, PLA2G7, UGDH, GCLC, PPP1R3C, NTRK1, PPARG, JMJD7, PLA2G4B, ABCC3, UGT1A6, CPT1A, PARD3, NRG1, H6PD, SLC5A3, MYC |
Molecular Transport | 1.36E-06-1E-02 | GCK, PTTG1, CXCL12, LGALS1 | MYC, SLC5A3, ABCG5, EIF2S1, GMFB, H6PD, MAPK1, NRG1, PARD3, CPT1A, TFRC, ABCC3, PPARG, AQP8, ABCC4, PPP1R3C, GCLC, ADM, NQO1 |
Cellular Growth and Proliferation | 1.25E-05-1E-02 | LGALS1, COL1A1, CCND2, KIF20A, CXCL12, CCNB1, RARB, PTTG1, LZTS1, HSD11B2, DLC1, COL1A2, BCL2A1, CDC2, INPP5 D, MMP2 | MYC, DNAJB6, NRG2 (includes EG:9542), CES2 (includes EG:8824), MAFF, CDH4 (includesEG:1002), UGT2B17, MAPK1, NRG1, TRIM35, TFRC, PPARG, CXCL2, ALDH1L1, CREG1, GSTP1, HMGCR, NTRK1, CDA, PHLDA1, PFN2, GRIN2C, ADM, CYP1A1 |
Cell Death | 3.45E-05-1E-02 | LGALS1, CYP26B1, CCND2, CKAP2, CXCL12, CCNB1, RARB, PTTG1, HSD11B2, DLC1, BCL2A1, CDC2, INPP5 D, MMP2 | MYC, DNAJB6, EIF2S1, DNM1L, NRG2(includes EG:9542), GMFB, HTATIP2, MAPK1, NRG1, TRIM35, TFRC, EPHX1, PPARG, CXCL2, SQSTM1, CYP2F1, GSTP1, GSR, NTRK1, ABCC4, PHLDA1, GCLC, PLA2G7, TXNRD1, NR1I3, GRIN2C, ADM, NQO1, NCF2 |
DNA Replication, Recombination, and Repair | 1.52E-04-1E-02 | LGALS1, CCND2, CXCL12, ECT2, CCNB1, PTTG1, MMP2 | MYC, NRG2 (includes EG:9542), PDE5A, NRG1, PPARG, RIOK3, GSTP1, GCLC, NR1I3, ADM, AMPD3, NQO1 |
Lipid Metabolism | 2.6E-04-1E-02 | GCK, INPP5 D, HSD11B2, CXCL12, PNPLA3, LGALS1 | CYP1A1, ADM, PLA2G7, PPP1R3C, UGT2B7, NTRK1, ACOT4, GSTP1, AQP8, PPARG, JMJD7-PLA2G4B, ABCC3, RDH16, CPT1A, MAPK1, H6PD, UGT2B17, CYP3A43, CYP2C18, ABCG5, MYC |
Cellular Assembly and Organization | 5.88E-04-1E-02 | LGALS1, COL1A1, ECT2, CCNB1, PTTG1, COL1A2, CDC2, KRT20, INPP5D | MYC, DNAJB6, DNM1L, EPB41, NRG1, RIOK3, PFN2, ADM |
Immune Cell Trafficking | 3.58E-03-1E-02 | COL1A1, CYTIP, CXCL12 | CXCL2 |
Humoral Immune Response | 5.57E-03-1E-02 | CXCL12, BCL2A1, NPP5D | MYC, NTRK1 |