Table 2.
Significantly upregulated genes in Group A EPN from enriched STAT3 and IL-6 pathway genesets.
| Gene symbol |
Gene title | FC | p-value | q-value |
|---|---|---|---|---|
| MSigDB C3: motif genesets: transcription factor targets: V$STAT3_01 genes | ||||
| CCL2 | chemokine (C-C motif) ligand 2 | 21.62 | 1.39E-08 | 3.67E-06 |
| IRF1 | interferon regulatory factor 1 | 8.66 | 8.48E-08 | 1.11E-05 |
| ICAM1 | intercellular adhesion molecule 1 | 8.32 | 2.11E-07 | 2.00E-05 |
| MAFF | v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (avian) | 15.87 | 7.78E-07 | 5.19E-05 |
| SERPING1 | serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 | 3.11 | 6.45E-06 | 0.000264 |
| CISH | cytokine inducible SH2-containing protein | 2.24 | 2.45E-05 | 0.000737 |
| APBA1 | amyloid beta (A4) precursor protein-binding, family A, member 1 | 1.93 | 0.00496 | 0.0393 |
| Experimentally determined STAT3 upregulated genes (Yu et al [REF]) | ||||
| IL8 | interleukin 8 | 24.13 | 5.22E-09 | 2.17E-06 |
| CCL2 | chemokine (C-C motif) ligand 2 | 21.62 | 1.39E-08 | 3.67E-06 |
| SOCS3 | suppressor of cytokine signaling 3 | 14.61 | 1.88E-08 | 4.35E-06 |
| TIMP1 | TIMP metallopeptidase inhibitor 1 | 5.49 | 3.65E-08 | 6.76E-06 |
| ICAM1 | intercellular adhesion molecule 1 | 8.32 | 2.11E-07 | 2E-05 |
| CHI3L1 | chitinase 3-like 1 (cartilage glycoprotein-39); YKL-40 | 40.27 | 2.87E-07 | 2.51E-05 |
| VEGFA | vascular endothelial growth factor A | 4.71 | 9.77E-07 | 6.07E-05 |
| PTGS2 | prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase); COX-2 | 10.57 | 2.82E-06 | 0.000142 |
| STAT3 | signal transducer and activator of transcription 3 (acute-phase response factor) | 1.63 | 3.72E-06 | 0.000176 |
| MCL1 | myeloid cell leukemia sequence 1 (BCL2-related) | 1.65 | 7.74E-06 | 0.00031 |
| VIM | vimentin | 1.41 | 8.05E-06 | 0.000318 |
| IL6 | interleukin 6 (interferon, beta 2) | 13.41 | 1.02E-05 | 0.000381 |
| BIRC3 | baculoviral IAP repeat-containing 3 | 5.94 | 6.29E-05 | 0.001533 |
| MMP9 | matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) | 7.96 | 6.32E-05 | 0.00154 |
| JAK3 | Janus kinase 3 | 3.56 | 6.54E-05 | 0.00157 |
| CXCL10 | chemokine (C-X-C motif) ligand 10 | 7.40 | 0.000143 | 0.00281 |
| LIF | leukemia inhibitory factor (cholinergic differentiation factor) | 3.88 | 0.000153 | 0.00298 |
| MMP2 | matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) | 2.59 | 0.00111 | 0.0134 |
| CCL5 | chemokine (C-C motif) ligand 5 | 2.28 | 0.00405 | 0.0340 |
| MYC | v-myc myelocytomatosis viral oncogene homolog (avian) | 2.09 | 0.00414 | 0.0345 |
| IL1B | interleukin 1, beta | 3.10 | 0.0064 | 0.0474 |
| MSigDB C2: curated genesets: BioCarta: IL6_PATHWAY genes | ||||
| MAP2K1 | mitogen-activated protein kinase kinase 1 | 1.80 | 3.65E-06 | 0.000174 |
| STAT3 | signal transducer and activator of transcription 3 (acute-phase response factor) | 1.63 | 3.72E-06 | 0.000176 |
| SHC1 | SHC (Src homology 2 domain containing) transforming protein 1 | 2.51 | 5.35E-06 | 0.000226 |
| IL6 | interleukin 6 (interferon, beta 2) | 13.41 | 1.02E-05 | 0.000381 |
| CEBPB | CCAAT/enhancer binding protein (C/EBP), beta | 2.01 | 4.38E-05 | 0.00114 |
| JAK3 | Janus kinase 3 | 3.56 | 6.54E-05 | 0.00157 |
| ELK1 | ELK1, member of ETS oncogene family | 1.42 | 0.000123 | 0.00251 |
| SRF | serum response factor (c-fos serum response element-binding transcription factor) | 1.77 | 0.000234 | 0.00409 |
| MAPK3 | mitogen-activated protein kinase 3 | 1.53 | 0.000782 | 0.0104 |
| JUN | jun proto-oncogene | 1.70 | 0.000952 | 0.0120 |
| FOS | FBJ murine osteosarcoma viral oncogene homolog | 3.99 | 0.00140 | 0.0159 |
FC, fold change