Table 3.
Network pathway annotation terms enriched in rapamycin up-regulated genes. Genes ≥5 fold upregulated in response to rapamycin treatment were analyzed for enrichment of KEGG terms. The identified enriched pathway annotation terms (GeneSet) from network analyses are listed. The total number of genes from the network identified to be up-regulated in response to rapamycin and belonging to a specific pathway were identified. p-value (with 0 values equating to<0.0001) and false discovery rates (FDR) are presented. Nodes identify the genes/proteins from our data sets present in the networks. Only the top 20 most significant annotations are shown.
| GeneSet | Genes From Network | p-value | FDR | Nodes |
|---|---|---|---|---|
| Cytokine-cytokine receptor interaction | 13 | 0 | <1.000e-03 | IL6ST,IL11,IL1B,INHBA,CXCL1,CXCL3,CXCL2,LIF,IFNA1,IL6,BMP2,IL8,TGFBR1 |
| Salmonella infection | 8 | 0 | <5.000e-04 | IL1B,ROCK2,PKN2,CXCL1,CXCL3,CXCL2,IL6,IL8 |
| Pathways in cancer | 12 | 0 | 3.33E-04 | FGF7,PTGS2,TPR,FGF2,MDM2,LAMC2,ITGAV,IL6,BMP2,IL8,TGFBR1,ITGA2 |
| Legionellosis | 6 | 0 | 2.50E-04 | IL1B,CXCL1,CXCL3,CXCL2,IL6,IL8 |
| Signaling by SCF-KIT | 8 | 0 | 2.00E-04 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF,JAK2 |
| IL23-mediated signaling events | 5 | 0 | 1.67E-04 | IL1B,CXCL1,CD4,IL6,JAK2 |
| PIP3 activates AKT signaling | 7 | 0 | 1.43E-04 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Validated transcriptional targets of AP1 family members Fra1 and Fra2 | 5 | 0 | 2.50E-04 | LIF,NFATC2,IVL,IL6,IL8 |
| Signaling by ERBB4 | 8 | 0 | 2.22E-04 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF,JAK2 |
| TNF signaling pathway | 7 | 0 | 3.00E-04 | PTGS2,IL1B,CXCL1,CXCL3,CXCL2,LIF,IL6 |
| PI3K-Akt signaling pathway | 11 | 0 | 3.64E-04 | FGF7,FGF2,PKN2,MDM2,LAMC2,IFNA1,ITGAV,IL6,ITGA2,NR4A1,JAK2 |
| IL27-mediated signaling events | 4 | 0 | 8.33E-04 | IL6ST,IL1B,IL6,JAK2 |
| ErbB4 signaling events | 4 | 0 | 8.46E-04 | NRG1,MDM2,HBEGF,JAK2 |
| NOD-like receptor signaling pathway | 5 | 0 | 8.57E-04 | IL1B,CXCL1,CXCL2,IL6,IL8 |
| Interleukin-6 signaling | 3 | 0.0001 | 1.27E-03 | IL6ST,IL6,JAK2 |
| Signaling by FGFR | 7 | 0.0001 | 1.94E-03 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Signaling by ERBB2 | 7 | 0.0001 | 1.88E-03 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| ErbB receptor signaling network | 3 | 0.0002 | 3.00E-03 | NRG1,EREG,HBEGF |
| DAP12 interactions | 7 | 0.0002 | 2.75E-03 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Signaling by EGFR | 7 | 0.0002 | 2.75E-03 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Signaling by PDGF | 7 | 0.0002 | 3.29E-03 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Cell junction organization | 5 | 0.0002 | 3.91E-03 | CLDN4,F11R,LAMC2,LIMS1,CLDN14 |
| Haematopoietic cell lineage | 5 | 0.0003 | 5.04E-03 | IL11,IL1B,CD4,IL6,ITGA2 |
| Rheumatoid arthritis | 5 | 0.0004 | 5.46E-03 | IL11,IL1B,CXCL1,IL6,IL8 |
| NF-kappa B signaling pathway | 5 | 0.0004 | 5.60E-03 | PTGS2,IL1B,CXCL2,IL8,ATM |
| Cell adhesion molecules (CAMs) | 6 | 0.0004 | 6.08E-03 | CLDN4,F11R,CLDN14,ITGAV,CD4,CD274 |
| p53 pathway feedback loops 2 | 3 | 0.0006 | 9.15E-03 | MDM2,ATR,ATM |
| Jak-STAT signaling pathway | 6 | 0.0007 | 9.57E-03 | IL6ST,IL11,LIF,IFNA1,IL6,JAK2 |
| Glypican 1 network | 3 | 0.0007 | 9.41E-03 | NRG1,FGF2,TGFBR1 |
| Proteoglycans in cancer | 7 | 0.0008 | 1.09E-02 | FGF7,FGF2,ROCK2,MDM2,ITGAV,ITGA2,HBEGF |
| Amoebiasis | 5 | 0.0009 | 1.13E-02 | IL1B,LAMC2,CXCL1,IL6,IL8 |
| BARD1 signaling events | 3 | 0.001 | 1.33E-02 | TOPBP1,ATR,ATM |
| Epithelial cell signaling in Helicobacter pylori infection | 4 | 0.0012 | 1.46E-02 | F11R,CXCL1,IL8,HBEGF |
| Transcriptional misregulation in cancer | 6 | 0.0013 | 1.56E-02 | BMI1,MDM2,JMJD1C,IL6,IL8,ATM |
| Fc epsilon receptor (FCERI) signaling | 8 | 0.0015 | 1.66E-02 | FGF7,NRG1,FGF2,EREG,MDM2,NFATC2,NR4A1,HBEGF |
| Chemokine signaling pathway | 6 | 0.0018 | 1.96E-02 | ROCK2,CXCL1,CXCL3,CXCL2,IL8,JAK2 |
| signal transduction through il1r | 3 | 0.0018 | 1.92E-02 | IL1B,IFNA1,IL6 |
| Glucocorticoid receptor regulatory network | 4 | 0.0019 | 1.99E-02 | MDM2,IL6,IL8,NR4A1 |
| ATR signaling pathway | 3 | 0.0021 | 2.14E-02 | TOPBP1,MDM2,ATR |
| TGF-β signaling pathway | 4 | 0.0022 | 2.11E-02 | GDF6,INHBA,BMP2,TGFBR1 |
| TGF-β signaling pathway | 4 | 0.0022 | 2.11E-02 | GDF6,INHBA,BMP2,TGFBR1 |
| Signaling by NGF | 7 | 0.0028 | 2.59E-02 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Small cell lung cancer | 4 | 0.0028 | 2.59E-02 | PTGS2,LAMC2,ITGAV,ITGA2 |
| il 6 signaling pathway | 2 | 0.0031 | 2.74E-02 | IL6,JAK2 |
| Hepatitis B | 5 | 0.0031 | 2.78E-02 | IFNA1,NFATC2,IL6,IL8,TGFBR1 |
| Validated transcriptional targets of deltaNp63 isoforms | 3 | 0.0034 | 2.86E-02 | NRG1,MDM2,ATM |
| p53 pathway | 3 | 0.0034 | 2.86E-02 | MDM2,ATR,ATM |
| Fanconi anemia pathway | 3 | 0.0036 | 2.97E-02 | TOPBP1,ATR,ATM |
| Calcineurin-regulated NFAT-dependent transcription in lymphocytes | 3 | 0.0038 | 3.06E-02 | PTGS2,NFATC2,IL8 |
| IL6-mediated signaling events | 3 | 0.0041 | 3.11E-02 | IL6ST,IL6,JAK2 |
| Integrins in angiogenesis | 3 | 0.0041 | 3.11E-02 | FGF2,F11R,ITGAV |
| Malaria | 3 | 0.0046 | 3.39E-02 | IL1B,IL6,IL8 |
| atm signaling pathway | 2 | 0.0047 | 3.40E-02 | MDM2,ATR |
| Sumoylation by RanBP2 regulates transcriptional repression | 2 | 0.0047 | 3.40E-02 | RANBP2,MDM2 |
| SHP2 signaling | 3 | 0.0051 | 3.64E-02 | IL6ST,IL6,JAK2 |
| Chagas disease (American trypanosomiasis) | 4 | 0.0055 | 3.85E-02 | IL1B,IL6,IL8,TGFBR1 |
| Toll-like receptor signaling pathway | 4 | 0.0059 | 4.11E-02 | IL1B,IFNA1,IL6,IL8 |
| Beta5 beta6 beta7 and beta8 integrin cell surface interactions | 2 | 0.006 | 4.08E-02 | ITGAV,TGFBR1 |
| cell cycle: g2/m checkpoint | 2 | 0.006 | 4.08E-02 | MDM2,ATR |
| Signaling by the B Cell Receptor (BCR) | 7 | 0.0064 | 4.33E-02 | FGF7,NRG1,FGF2,EREG,MDM2,NR4A1,HBEGF |
| Influenza A | 5 | 0.0068 | 4.51E-02 | IL1B,IFNA1,IL6,IL8,JAK2 |
| Meiotic Synapsis | 3 | 0.0069 | 4.45E-02 | H2AFB1,ATR,SYNE1 |
| p53 pathway | 3 | 0.0069 | 4.45E-02 | MDM2,ATR,ATM |