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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
  1. * Full names of the genes are listed in Additional file 1, Table S 1.