Table 1. DEGs involved in inflammatory/immune response.
This table was provided by checking the differentially expressed hub genes in all networks for being involved in inflammatory/immune response. In addition, we checked to datasets to detect if hub genes in this study are also deregulated in others. Abbreviations: PPI: Protein-Protein Interaction; WGCNA: Weighted Gene Co-expression Network Analysis; DCs: Dendritic Cells; NTs: Neutrophils; PBMCs: Peripheral Blood Mononuclear Cells.
| Cell Type | Gene symbol | Log2FC (This study) | WGCNA (Hubs) | PPI network (Module No.) | PPI network (Hubs) | TFs from GRN | GSE26378 (Log2FC) | GSE54514 (Log2FC) | PMCID/PMID |
|---|---|---|---|---|---|---|---|---|---|
| DCs | ADORA3* | 1.30 | ✓ | - | - | NR1H3 | 1.40 | - | 10660615 |
| ATF3 | -0.97 | - | ✓ | - | ATF3 | - | - | PMC2783469 | |
| CD163 | 1.37 | ✓ | - | - | - | 2.39 | - | PMC3638564 | |
| CD163L1 | 1.06 | ✓ | - | - | - | - | - | 25877931 | |
| CD83 | -0.99 | ✓ | - | - | RUNX2 | - | - | 23787022 | |
| FKBP5 | 1.42 | ✓ | - | - | NR1H3, RUNX2 | 2.26 | - | PMC4156438 | |
| SATB1 | -0.71 | ✓ | - | - | RUNX2 | -1.01 | - | 26667169 | |
| SOCS1 | 0.77 | - | ✓ (M2) | ✓ | - | - | 0.70 | PMC5499360 | |
| TIMP3 | -1.42 | ✓ | ✓ | - | - | - | - | 16393953 | |
| TNFRSF9 | -1.02 | ✓ | ✓ | - | KLF4, ATF3 | - | - | 7678621 | |
| NTs | ADORA3 | 1.09 | ✓ | - | - | - | 1.40 | - | 10660615 |
| CCL3 | -1.27 | ✓ | ✓ | - | - | - | - | PMC98771 | |
| CD300LF | -0.84 | ✓ | - | - | - | 1.17 | - | PMC3596959 | |
| CD83 | -0.85 | ✓ | - | - | - | - | - | 23787022 | |
| CDKN1A | -0.80 | - | ✓ (8) | ✓ | SMAD3 | - | - | 12972156 | |
| CEBPD | 1.32 | ✓ | ✓ | - | BCOR | 1.54 | - | 9792624 | |
| CLEC4D | 1.47 | ✓ | - | - | - | 2.96 | - | PMC4589735 | |
| CRISPLD2 | 0.66 | ✓ | - | - | - | - | - | PMC5027350 | |
| ELK1 | -0.9 | ✓ | ✓ | - | - | - | - | PMC5519339 | |
| FKBP5 | 2.81 | ✓ | ✓ (8) | - | - | 2.26 | - | PMC4156438 | |
| GNAQ | 1.07 | - | ✓ | ✓ | - | 1.31 | - | PMC4068741 | |
| HVCN1 | -0.61 | ✓ | - | - | - | -0.93 | - | PMC4172129 | |
| IL1B | -1.39 | - | ✓ (4) | ✓ | - | 1.15 | - | PMC3083294 | |
| JUN | -0.66 | - | ✓ | ✓ | - | - | - | 21339212 | |
| MAP2K1 | 0.99 | - | ✓ | ✓ | - | - | - | 10679258 | |
| MAPK14 | 0.86 | - | ✓ | ✓ | BCOR | 2.38 | -0.83 | PMC4264013 | |
| NLRP6 | 1.27 | ✓ | ✓ | - | - | - | - | PMC3810296 | |
| RNASE6 | 1.17 | ✓ | - | - | - | -0.79 | - | PMC4281292 | |
| SH2B3 | -0.92 | ✓ | - | - | - | - | - | PMC4393357 | |
| SMAD3 | -0.68 | - | ✓ | ✓ | SMAD3 | -0.91 | - | PMC3634534 | |
| SRC | -1.67 | - | ✓ | ✓ | - | - | - | PMC3893689 | |
| TOB1 | 1.27 | ✓ | ✓ | - | SMAD3 | - | - | PMC4111268 | |
| PBMCs | ADORA3 | 1.75 | ✓ | - | - | GATA2 | 1.40 | - | 10660615 |
| ATF3 | -0.77 | - | ✓ | - | ATF3 | - | - | PMC2783469 | |
| CCL3 | -0.68 | ✓ | ✓ | - | ATF3 | - | - | PMC98771 | |
| CD40 | -0.74 | ✓ | - | - | - | - | - | PMC4831216 | |
| CD83 | -0.72 | ✓ | - | - | - | - | - | 23787022 | |
| CD163 | 2.38 | ✓ | - | - | - | 2.39 | - | PMC3638564 | |
| CEBPD | 0.84 | ✓ | ✓ (4) | - | - | 1.54 | - | 9792624 | |
| CXCL11 | -1.82 | ✓ | ✓ (2) | - | - | - | - | PMC4348563 | |
| CXCR5 | -0.77 | - | ✓ (2) | ✓ | - | - | - | PMC2759473 | |
| FASLG | -0.67 | ✓ | ✓ (6) | - | - | - | - | PMC3519983 | |
| FFAR2 | -1.24 | ✓ | ✓ (3) | - | - | 1.70 | -0.82 | PMC4734206 | |
| GATA2 | -0.85 | - | - | - | GATA2 | -0.62 | - | PMC4409096 | |
| GBP1 | -1.03 | ✓ | ✓ (1) | ATF3 | - | - | PMC5307439 | ||
| GBP4 | -1.05 | ✓ | ✓ (1) | - | -0.83 | - | PMC3570361 | ||
| GBP5 | -1.07 | ✓ | ✓ (1) | - | ATF3 | - | - | 26996307 | |
| IDO1 | -1.31 | ✓ | - | - | ATF3 | - | - | PMC4586474 | |
| IFI35 | -0.62 | ✓ | ✓ (1) | - | - | 0.95 | - | PMC5643540 | |
| IFIH1 | -0.62 | ✓ | - | - | - | - | - | PMC3262963 | |
| ISG15 | -1.00 | ✓ | ✓ (1) | - | - | - | 2.5 | PMC522249 | |
| LTB | -0.84 | ✓ | - | - | - | -0.81 | -0.88 | 12474234 | |
| OAS2 | -0.97 | ✓ | ✓ (1) | - | - | - | 2.17 | PMC4351405 | |
| RIPK2 | -0.61 | ✓ | ✓ (6) | - | - | - | - | PMC4579271 | |
| SAMD9L | -0.76 | ✓ | - | - | - | 0.78 | 1.14 | PMC5399482 | |
| SIGLEC9 | 0.69 | ✓ | - | - | - | 1.56 | - | 10801862 | |
| SLA | 0.61 | ✓ | - | - | - | 1.24 | - | PMC4137477 | |
| SLAMF7 | -1.09 | ✓ | - | - | - | - | - | 23695528 | |
| STAT1 | -0.60 | - | ✓ (1) | ✓ | - | - | 0.89 | PMC3670275 | |
| TLR7 | -1.19 | ✓ | - | - | - | -0.63 | - | 15585605 | |
| TNFRSF9 | -0.94 | ✓ | ✓ | - | ATF3 | - | - | PMC3104000 |
* Bold symbols shows repetitive genes in all cell types.