Table 2.
Canonical Pathways identified by IPA from the probe sets (1222) that were differentially expressed after MTX compared to before MTX, (n=11 cases, 22 datasets). P values are for the pathway as a whole.
| Pathway | p-value | Molecules |
|---|---|---|
| PI3K/AKT Signaling | 0.003 | RELA, JAK1, FOXO1, SOS1, LIMS1, MAP3K8, GSK3A, ITGA3, RHEB, EIF4E, PTEN |
| Cdc42 Signaling | 0.005 | ACTR2, DIAPH1, CDC42BPA, TNK2, EXOC7, MYL10, ITGA3, IQGAP1, CLIP1, LIMK1 |
| IL-9 Signaling | 0.005 | SOCS3, RELA, JAK1, IRS2, STAT5B |
| Insulin Receptor Signaling | 0.006 | SOCS3, PPP1R3D, JAK1, CBL, PPP1R10, FOXO1, SOS1, IRS2, GSK3A, EIF4E, PTEN |
| Glycosphingolipid Biosynthesis – Lactoseries | 0.009 | FUT2, FUT6, ST3GAL3 |
| Protein Kinase A Signaling | 0.009 | RELA, CREM, PDE7A, ITPR2, GSK3A, PLCL2, TTN, ROCK1, GNB4, GNAS, PPP1R3D, NFAT5, PPP1R10, TGFB2, ADD1, LEF1, MYL10, GNG12, PRKCB |
| iCOS-iCOSL Signaling in T Helper Cells | 0.010 | PTPRC, ICOS, RELA, NFAT5, CD40, ITPR2, PLEKHA2, ICOSLG, PTEN |
| Thrombin Signaling | 0.010 | RELA, F2RL2, ITPR2, PLCL2, ROCK1, GNAS, GNB4, RHOB, GNAT2, ARHGEF16, SOS1, MYL10, GNG12, PRKCB |
| Ephrin Receptor Signaling | 0.011 | ACTR2, ITGA3, PDGFB, FGF1, LIMK1, ROCK1, GNAS, GNB4, GNAT2, EFNA5, ACP1, SOS1, GNG12 |
| IL-4 Signaling | 0.011 | B2M, SOCS1, IL4R, NFAT5, JAK1, IRF4, SOS1 |
| ATM Signaling | 0.011 | SMC3, GADD45A, TLK1, CCNB2, CDC2, SMC1A |
| Apoptosis Signaling | 0.012 | ROCK1, CAPN5, RELA, CASP3, CASP2, CYCS, CAPN2, CDC2 |
| Glycosphingolipid Biosynthesis | 0.015 | GCNT4, ST8SIA1, FUT2, FUT6 |
| fMLP Signaling in Neutrophils | 0.017 | NOX1, GNAS, ACTR2, RELA, GNB4, NFAT5, ITPR2, GNG12, PRKCB |
| PTEN Signaling | 0.017 | RELA, CBL, CASP3, FOXO1, SOS1, GSK3A, ITGA3, PTEN |
| Primary Immunodeficiency Signaling | 0.019 | PTPRC, ICOS, CD40, IGL, IGHG1 |
| Integrin Signaling | 0.022 | CAPN5, ACTR2, LIMS1, TNK2, ITGA3, TTN, PTEN, ROCK1, ARF1, RHOB, SOS1, CAV1, CAPN2 |
| Molecular Mechanisms of Cancer | 0.024 | RELA, TCF4, JAK1, CASP3, GSK3A, AURKA, TCF3, GNAS, CBL, RHOB, FOXO1, ARHGEF16, GNAT2, SOS1, TGFB2, CYCS, LEF1, HIPK2, MAP3K7IP1, PRKCB |
| Erythropoietin Signaling | 0.035 | SOCS3, RELA, CBL, SOS1, STAT5B, PRKCB |
| Angiopoietin Signaling | 0.035 | RELA, FOXO1, SOS1, STAT5B, BIRC5, TIE1 |
| Cardiac Hypertrophy Signaling | 0.035 | CACNA1D, PLCL2, EIF4E, ROCK1, GNAS, GNB4, RHOB, GNAT2, SOS1, TGFB2, MAP3K8, MYL10, MAP3K7IP1, GNG12 |
| DNA Methylation & Transcriptional Repression | 0.037 | CHD4, ARID4B, RBBP4 |
| Oncostatin M Signaling | 0.037 | JAK1, SOS1, PLAU, STAT5B |
| CD27 Signaling in Lymphocytes | 0.042 | RELA, CASP3, CYCS (includes EG:54205), MAP3K8, MAP2K5 |
| PDGF Signaling | 0.042 | JAK1, ACP1, SOS1, CAV1, PDGFB, PRKCB |
| Actin Cytoskeleton Signaling | 0.043 | ACTR2, ITGA3, IQGAP1, PDGFB, TTN, FGF1, LIMK1, ROCK1, DIAPH1, SOS1, WASF2, MYL10, GNG12 |
| RhoA Signaling | 0.044 | ROCK1, ACTR2, RHPN1, SEPT7, MYL10, SEPT2, TTN, LIMK1 |
| One Carbon Pool by Folate | 0.048 | TYMS, MTHFD1L, GART |