Table 1.
List of MetaCore pathways obtained by an enrichment analysis of 6950 upregulated genes in livers treated with u-ADSCs (downregulated in untreated livers (PBS)) identified in a preliminary class comparison (parametric p < 0.05).
| # | Maps | Total | p value | FDR | In Data | Network Objects from Active Data |
|---|---|---|---|---|---|---|
| 1 | Development_VEGF signaling via VEGFR2 - generic cascades | 93 | 3.060E-11 | 4.505E-08 | 38 | RhoA, Pyk2(FAK2), PI3K cat class IA, NCK1, CCL2, H-Ras, PAK2, MEK3(MAP2K3), TCF7L2 (TCF4), ROCK1, eIF4E, ERK1/2, VEGF-A, c-Raf-1, VEGFR-2, SOS, MNK1, p90Rsk, Paxillin, IP3 receptor, Shc, p120GAP, PKC, PI3K reg class IA, Vinculin, PKC-alpha, alpha-V/beta-3 integrin, HSP27, MEK2(MAP2K2), FAK1, IKK-gamma, CREB1, Neurofibromin, ERK2 (MAPK1), AKT(PKB), HSP90, Calcineurin B (regulatory), NF-AT2(NFATC1) |
| 2 | CFTR folding and maturation (normal and CF) | 24 | 1.511E-10 | 1.005E-07 | 17 | PARP-1, GANAB, UGCGL1, EDEM, HSP105, HSP90 alpha, CFTR, Hdj-2, Sti1, HSP90 beta, Aha1, HSPBP1, HSP40, Calnexin, HSP70, BAG-3, p23 co-chaperone |
| 3 | Chemotaxis_Lysophosphatidic acid signaling via GPCRs | 129 | 2.657E-10 | 1.005E-07 | 45 | RhoA, E-cadherin, cPKC (conventional), PLD1, PI3K cat class IA (p110-beta), Tcf(Lef), H-Ras, TRAF6, ROCK1, MKL2, ERK1/2, PKC-zeta, c-Raf-1, G-protein alpha-q/11, PKC-epsilon, TRIP6, CD36, Paxillin, IP3 receptor, LPAR2, MLCP (reg), ROCK, PI3K reg class IA (p85), Caspase-7, PAK, PDZ-RhoGEF, PKC, PLC-beta, Vinculin, ATF-2, DIA1, HAS2, alpha-V/beta-3 integrin, FasR(CD95), FAK1, CREB1, Bcl-XL, MEK1/2, Rho GTPase, N-CoR, JNK(MAPK8-10), MKL1, AKT(PKB), p53, Elk-1 |
| 4 | Transport_Clathrin-coated vesicle cycle | 71 | 2.731E-10 | 1.005E-07 | 31 | Syntaxin 6, Rab-4, VTI1A, Myosin I, Rabaptin-5, HIP1, Rab11-FIP1, PIP5KIII, Rab-8, Eps15, SNX9, VAMP4, Dynamin-2, Actin, YKT6, GS15, RAB9P40, Rab-7, Rab-11A, Endophilin B1, PLEKHA8 (FAPP2), Rab11-FIP2, VPS45A, PREB, BIN1 (Amphiphysin II), EEA1, Clathrin, Syntaxin 16, Myosin Vb, Clathrin heavy chain, VAMP2 |
| 5 | Development_The role of GDNF ligand family/RET receptor in cell survival, growth and proliferation | 92 | 1.837E-09 | 5.408E-07 | 35 | RhoA, PI3K cat class IA, B-Raf, NCK1, IRS-1, H-Ras, ATF-1, ERK1/2, VEGF-A, c-Raf-1, SOS, Paxillin, IP3 receptor, CDK2, Shc, ROCK, PI3K reg class IA (p85), MLC2, CREM (activators), SHP-2, alpha-V/beta-3 integrin, N-Ras, CaMK II alpha, VAV-2, FAK1, IKK-gamma, CREB1, Bcl-XL, MEK1/2, Cyclin D1, JNK2(MAPK9), NF-kB, c-FLIP, AKT(PKB), Elk-1 |
| 6 | Cytoskeleton remodeling_FAK signaling | 57 | 2.384E-09 | 5.848E-07 | 26 | RhoA, PI3K cat class IA, Cyclin D3, TRAF3, H-Ras, DOCK1, ERK1/2, p190RhoGAP, VEGF-A, c-Raf-1, VEGFR-2, SOS, G-protein alpha-q/11, FARP2, Paxillin, IP3 receptor, Talin, Shc, PI3K reg class IA, PLC-beta, PTEN, RIPK1, MEK2(MAP2K2), FAK1, AKT(PKB), Elk-1 |
| 7 | Immune response_TCR alpha/beta signaling pathway | 97 | 9.339E-09 | 1.922E-06 | 35 | STIM1, STIM2, B-Raf, CD45, TRAF3, TRAF2, H-Ras, TRAF6, ERK1/2, CABIN1, c-FLIP(Long), E2N(UBC13), c-Raf-1, Ca(II)channel L-type, Csk, Pannexin-1, Caspase-8, GRAP2, IP3 receptor, MEF2D, ORAI1, PKC-theta, PAG, PKC-alpha, CD3, CalDAG-GEFII, P2X1, RIPK1, CFLAR p43, IKK-gamma, MEK1/2, AKT(PKB), UEV1A, Calcineurin B (regulatory), NF-AT2(NFATC1) |
| 8 | IL-6 signaling in breast cancer cells | 53 | 1.175E-08 | 1.922E-06 | 24 | N-cadherin, E-cadherin, PI3K cat class IA, IP10, NF-kB1 (p50), H-Ras, ERK1/2, c-Raf-1, SOS, HSD17B1, MDR1, STAT1, Shc, PI3K reg class IA, SHP-2, Fascin, IL-6, Bcl-XL, MEK1/2, AKT2, Cyclin D1, AKT(PKB), Jagged1, Mcl-1 |
| 9 | DNA damage_ATR activation by DNA damage | 53 | 1.175E-08 | 1.922E-06 | 24 | RAD17, HUWE1, ERK1/2, Histone H2AX, Rad50, PRMT5, RAD9A, CINP, HSP90 beta, p90Rsk, RAD9, p53BP1, EGLN3, MRN complex, TTI1, Casein kinase II, NEK1, TELO2, TTI2, ETAA1, PP5, USP20 (VDU2), Nibrin, DBC1 |
| 10 | Chemotaxis_SDF-1/CXCR4-induced chemotaxis of immune cells | 79 | 2.754E-08 | 4.055E-06 | 30 | RhoA, Pyk2(FAK2), PI3K cat class IA, VCAM1, CD45, CALDAG-GEFI, NCK1, PLD1, ICAM1, PKA-cat alpha, PAK2, ROCK1, ERK1/2, PKC-zeta, PKA-reg (cAMP-dependent), Csk, JAK3, Paxillin, Talin, Shc, PI3K reg class IA (p85), PAK, PLC-beta, Vinculin, CD3, CD3 zeta, FAK1, MEK1/2, AKT(PKB), SFK |
| 11 | Immune response_B cell antigen receptor (BCR) pathway | 110 | 3.105E-08 | 4.154E-06 | 37 | STIM1, VCAM1, B-Raf, NCK1, NF-kB1 (p50), K-RAS, ICAM1, ETS1, H-Ras, PIP5KIII, MEK3(MAP2K3), ERK1/2, c-Raf-1, PP2A catalytic, BCAP, SOS1, PIP5KI, IP3 receptor, CDK6, Shc, PI3K reg class IA (p85), ORAI1, Rb protein, ATF-2, CalDAG-GEFII, N-Ras, VAV-2, MEK2(MAP2K2), GSK3 alpha/beta, IKK-gamma, Bcl-XL, MEK1/2, NF-kB, AKT(PKB), Calcineurin B (regulatory), Elk-1, NF-AT2(NFATC1) |
| 12 | G-protein signaling_K-RAS regulation pathway | 25 | 5.626E-08 | 6.902E-06 | 15 | B-Raf, CALDAG-GEFI, K-RAS, c-Raf-1, SOS, A-Raf-1, FTase, KAP3, Shc, PI3K cat class IA (p110-alpha), PKC-theta, RASSF1, Rap1GDS1, CalDAG-GEFII, RASGRF1 |
| 13 | Regulation of degradation of deltaF508-CFTR in CF | 39 | 9.216E-08 | 1.044E-05 | 19 | HSC70, HSP105, CFTR, HDAC6, Hdj-2, Sti1, SAE1, Dynein 1, cytoplasmic, heavy chain, Aha1, HSP27, HSPBP1, MJD (ataxin-3), BAG-2, UBE2J1, UBE2D1, HSP90, CHIP, HSP70, Derlin1 |
| 14 | Development_WNT/Beta-catenin signaling in the nucleus | 62 | 9.938E-08 | 1.045E-05 | 25 | TRRAP, TNIK, BAF53, PLD1, Tcf(Lef), TCF7L2 (TCF4), TBP, BRG1, MED1, PYGO2, BCL9/B9L, MEF2, TLE, DOT1, Kaiso, UBR5, hSPT3, RUNX, Pitx2, Casein kinase II, SET8, JNK(MAPK8-10), SMARCA5, EP400, RUVBL1 |
| 15 | Development_Positive regulation of STK3/4 (Hippo) pathway and negative regulation of YAP/TAZ function | 71 | 1.309E-07 | 1.258E-05 | 27 | RhoA, GCGR, E-cadherin, PKA-cat alpha, INADL, Alpha-1 catenin, 14-3-3, AMPK alpha subunit, PKA-reg (cAMP-dependent), MARKK, c-Raf-1, PP2A cat (alpha), Alpha-catenin, ZO-2, MOBKL1A, WW45, LATS1, Schwannomin (NF2), LKB1, STK4, RASSF1, FasR(CD95), Mol1b, Skp2/TrCP/FBXW, Beta-2 adrenergic receptor, Angiomotin (AMOT), PKA-cat (cAMP-dependent) |
| 16 | IL-6 signaling in multiple myeloma | 51 | 1.394E-07 | 1.258E-05 | 22 | PI3K cat class IA, K-RAS, ERK1/2, VEGF-A, c-Raf-1, VEGFR-2, SOS, STAT1, CDK6, Shc, PI3K reg class IA (p85), Rb protein, SHP-2, N-Ras, MEK2(MAP2K2), IL-6, Bcl-XL, Cyclin D1, JNK2(MAPK9), AKT(PKB), p53, Mcl-1 |
| 17 | Development_Fetal brown fat cell differentiation | 55 | 1.453E-07 | 1.258E-05 | 23 | PI3K cat class IA, SREBP1 (nuclear), IRS-1, H-Ras, ERK1/2, PKC-zeta, PKA-reg (cAMP-dependent), c-Raf-1, SOS, IGF-2 receptor, FASN, STAT5B, TR-beta, Prolactin receptor, SREBP1 precursor, Shc, PI3K reg class IA (p85), MEK2(MAP2K2), CREB1, AKT(PKB), PPAR-gamma, PKA-cat (cAMP-dependent), C/EBPalpha |
Abbreviations: u-ADSC, uncultured adipose tissue-derived stromal cells; PBS, phosphate-buffered saline; VEGF, vascular endothelial growth factor; CFTR, cystic fibrosis transmembrane conductance regulator; CF, cystic fibrosis; GPCRs, G protein-coupled receptors; GDNF, glial cell-derived neurotrophic factor; RET, rearranged during transfection; FAK, focal adhesion kinase; TCR, T-cell receptor; ATR, Rad3-related; SDF1, stromal cell-derived factor 1; CXCR-4, C-X-C chemokine receptor type 4.