Table 1.
Genes with potentially broad impact on the confrontation and the inhibitory capacity
| Gene | Method of prioritization | Role | Description |
|---|---|---|---|
| NFKBIA | Confrontation DEG | Co-regulated by RELA | nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha [Source: HGNC Symbol; Acc:7797] |
| IL1B | Confrontation DEG | Co-regulated by RELA | interleukin 1, beta [Source: HGNC Symbol; Acc:5992] |
| RELT | Confrontation DEG | Co-regulated by RELA | RELT tumor necrosis factor receptor [Source: HGNC Symbol; Acc:13764] |
| BHLHE40 | Confrontation DEG | Co-regulated by RELA | basic helix-loop-helix family, member e40 [Source: HGNC Symbol; Acc:1046] |
| FOS | Connected to confrontation DEGs | Transcription factor | FBJ murine osteosarcoma viral oncogene homolog [Source: HGNC Symbol; Acc:3796] |
| SRF | Connected to confrontation DEGs | Transcription factor | serum response factor (c-fos serum response element-binding transcription factor) [Source: HGNC Symbol; Acc:11291] |
| FOSB | Confrontation DEG | Co-regulated by RELA | FBJ murine osteosarcoma viral oncogene homolog B [Source: HGNC Symbol; Acc:3797] |
| CYR61 | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | cysteine-rich, angiogenic inducer, 61 [Source: HGNC Symbol; Acc:2654] |
| IKBKB | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta [Source: HGNC Symbol; Acc:5960] |
| IKBKE | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon [Source: HGNC Symbol; Acc:14552] |
| IKBKG | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma [Source: HGNC Symbol; Acc:5961] |
| IKBKG | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_b [Source: UniProtKB/TrEMBL; Acc:D3DWY0] |
| NR4A2 | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | nuclear receptor subfamily 4, group A, member 2 [Source: HGNC Symbol; Acc:7981] |
| PDGFRA | Connected to confrontation DEGs | Pro-inflammatory signature (Erez et al., 2012) | platelet-derived growth factor receptor, alpha polypeptide [Source: HGNC Symbol; Acc:8803] |
| ANXA4 | inhibition DEG | Co-regulated by FOXA1 | annexin A4 [Source: HGNC Symbol; Acc:542] |
| CDK6 | inhibition DEG | Co-regulated by FOXA1 | cyclin-dependent kinase 6 [Source: HGNC Symbol; Acc:1777] |
| KAZN | inhibition DEG | Co-regulated by FOXA1 | kazrin, periplakin interacting protein [Source: HGNC Symbol; Acc:29173] |
| RMND5A | inhibition DEG | Co-regulated by FOXA1 | required for meiotic nuclear division 5 homolog A (S. cerevisiae) [Source: HGNC Symbol; Acc:25850] |
| TNS3 | inhibition DEG | Co-regulated by FOXA1 | tensin 3 [Source: HGNC Symbol; Acc:21616] |
| IL6 | Connected to inhibition DEGs | Potential regulator | interleukin 6 (interferon, beta 2) [Source: HGNC Symbol; Acc:6018] |
| MAPK8 | Connected to inhibition DEGs | Potential regulator | mitogen-activated protein kinase 8 [Source: HGNC Symbol; Acc:6881] |
| MAP2K4 | Connected to inhibition DEGs | Potential regulator | mitogen-activated protein kinase kinase 4 [Source: HGNC Symbol; Acc:6844] |
| PRKCA | Connected to inhibition DEGs | Potential regulator | protein kinase C, alpha [Source: HGNC Symbol; Acc:9393] |
| YBX1 | Connected to inhibition DEGs | Transcription factor | Y box binding protein 1 [Source: HGNC Symbol; Acc:8014] |
| GFI1 | Connected to inhibition DEGs | Transcription factor | growth factor independent 1 transcription repressor [Source: HGNC Symbol; Acc:4237] |
| ESR1 | Connected to inhibition DEGs | Transcription factor | estrogen receptor 1 [Source: HGNC Symbol; Acc:3467] |
| ETS1 | Connected to inhibition DEGs | Transcription factor | v-ets avian erythroblastosis virus E26 oncogene homolog 1 [Source: HGNC Symbol; Acc:3488] |
| ETS2 | Connected to inhibition DEGs | Transcription factor | v-ets avian erythroblastosis virus E26 oncogene homolog 2 [Source: HGNC Symbol; Acc:3489] |
| AR | Connected to inhibition DEGs | Transcription factor | androgen receptor [Source: HGNC Symbol; Acc:644] |
| GATA1 | Connected to inhibition DEGs | Transcription fact or | GATA binding protein 1 (globin transcription factor 1) [Source: HGNC Symbol; Acc:4170] |
| GATA2 | Connected to inhibition DEGs | Transcription factor | GATA binding protein 2 [Source: HGNC Symbol; Acc:4171] |
| GATA3 | Connected to inhibition DEGs | Transcription factor | GATA binding protein 3 [Source: HGNC Symbol; Acc:4172] |
| PAX2 | Connected to inhibition DEGs | Transcription factor | paired box 2 [Source: HGNC Symbol; Acc:8616] |
| JUN | Connected to inhibition DEGs | Transcription factor | jun proto-oncogene [Source: HGNC Symbol; Acc:6204] |
| STAT3 | Connected to inhibition DEGs | Transcription factor | signal transducer and activator of transcription 3 (acute-phase response factor) [Source: HGNC Symbol; Acc:11364] |
| STAT5A | Connected to inhibition DEGs | Transcription factor | signal transducer and activator of transcription 5A [Source: HGNC Symbol; Acc:11366] |
| CAMK2A | Confrontation DEG | Involved in TGFbeta signaling, associated with survival | calcium/calmodulin-dependent protein kinase II alpha [Source: HGNC Symbol; Acc:1460] |
| CDK6 | Confrontation DEG | Involved in TGFbeta signaling, associated with survival | cyclin-dependent kinase 6 [Source: HGNC Symbol; Acc:1777] |
| CDKN2B | Confrontation DEG | Involved in TGFbeta signaling, associated with survival | cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) [Source: HGNC Symbol; Acc:1788] |
| NR4A1 | Confrontation DEG | Involved in TGFbeta signiling, associated with survival | nuclear receptor subfamily 4, group A, member 1 [Source: HGNC Symbol; Acc:7980] |
| SMAD3 | Confrontation DEG | Involved in TGFbeta signiling, associated with survival | SMAD family member 3 [Source: HGNC Symbol; Acc:6769] |
| TGFB1 | Confrontation DEG | Involved in TGFbeta signiling, associated with survival | transforming growth factor, beta 1 [Source: HGNC Symbol; Acc:11766] |
| TGFB3 | Confrontation DEG | Involved in TGFbeta signiling, associated with survival | transforming growth factor, beta 3 [Source: HGNC Symbol; Acc:11769] |
| EFNB2 | inhibition DEG | Associated with survival | ephrin-B2 [Source: HGNC Symbol; Acc:3227] |
| TMEM220 | inhibition DEG | Associated with survival | transmembrane protein 220 [Source: HGNC Symbol; Acc:33757] |
| TFAP2C | inhibition DEG | Associated with survival | transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source: HGNC Symbol; Acc:11744] |
| RPSAP52 | inhibition DEG | Associated with survival | ribosomal protein SA pseudogene 52 [Source: HGNC Symbol; Acc:35752] |
| SLC40A1 | inhibition DEG | Associated with survival | solute carrier family 40 (iron-regulated transporter), member 1 [Source: HGNC Symbol; Acc:10909] |
| CYP1B1 | inhibition DEG | Associated with survival | cytochrome P450, family 1, subfamily B, polypeptide 1 [Source: HGNC Symbol; Acc:2597] |
| CHAC1 | inhibition DEG | Associated with survival | ChaC, cation transport regulator homolog 1 (E. coli) [Source: HGNC Symbol; Acc:28680] |
| CCL2 | inhibition DEG | Associated with survival | chemokine (C-C motif) ligand 2 [Source: HGNC Symbol; Acc:10618] |
| PSAT1 | inhibition DEG | Associated with survival | phosphoserine aminotransferase 1 [Source: HGNC Symbol; Acc:19129] |
| RCAN2 | inhibition DEG | Associated with survival | regulator of calcineurin 2 [Source: HGNC Symbol; Acc:3041] |
| SCG2 | inhibition DEG | Associated with survival | secretogranin II [Source: HGNC Symbol; Acc:10575] |
| AEBP1 | inhibition DEG | Associated with survival | AE binding protein 1 [Source: HGNC Symbol; Acc:303] |
| MXRA8 | inhibition DEG | Associated with survival | matrix-remodelling associated 8 [Source: HGNC Symbol; Acc:7542] |
| TBC1D1 | inhibition DEG | Associated with survival | TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 [Source: HGNC Symbol; Acc:11578] |
| ITGA6 | inhibition DEG | Associated with survival | integrin, alpha 6 [Source: HGNC Symbol; Acc:6142] |
| PLAUR | inhibition DEG | Associated with survival | plasminogen activator, urokinase receptor [Source: HGNC Symbol; Acc:9053] |