Table 1.
Gene expression summary in naïve microglia. Differential analysis of the count data was done with the DESeq2 package; up regulated genes are highlighted in red and down regulated genes are highlighted in brown. Values in the column “naïve cells” correspond to fold change from the NC to NL (Cao et al., 2015).
| Relevance | Gene name (Human Orthologs) | Naïve cells |
|---|---|---|
| AMPK signaling pathway | PRKAA1 | 0.169 |
| PRKAA2 | 2.776 | |
| PRKAB1 | −0.189 | |
| PRKAB2 | 0.861 | |
| PRKAG1 | −0.379 | |
| PRKAG2 | −0.405 | |
| PRKAG3 | −1.329 | |
| Leptin | LEP | 5.033 |
| Adrenoceptor alpha 1A | ADRA1A | 2.572 |
| Adipocytokine signaling pathway | CAMKK1 | −1.110 |
| CAMKK2 | 0.660 | |
| Adiponectin | ADIPOQ | 2.422 |
| Calcium binding protein 39 | CAB39 | 0.279 |
| CAB39L | −0.076 | |
| Serine/threonine kinase 11 | STK11 | −0.178 |
| STE20-related kinase adaptor alpha | STRADA | −0.536 |
| STRADB | −0.506 | |
| Tak1 protein | MAP3K7 | −0.057 |
| Insulin signaling pathway | IGF1 | 1.601 |
| IGF1R | −0.125 | |
| IRS1 | 1.241 | |
| IRS4 | 4.420 | |
| PIK3-Akt signaling pathway | PIK3CA | 0.018 |
| PIK3CB | 1.793 | |
| PIK3CG | 1.950 | |
| PIK3R1 | 1.330 | |
| PIK3R3 | 1.083 | |
| PIK3R5 | 4.343 | |
| PDPK1 | 0.915 | |
| AKT2 | −0.335 | |
| AKT3 | 0.350 | |
| TSC1 | 1.099 | |
| TSC2 | 0.219 | |
| mTOR signaling pathway | RHEB | −0.257 |
| AKT1S1 | 0.908 | |
| MTOR | −0.107 | |
| RPTOR | 0.298 | |
| Inhibit cell growth and protein synthesis | RPS6KB1 | −0.078 |
| RPS6KB2 | −0.569 | |
| EIF4EBP1 | −0.822 | |
| PPARG2 | −2.093 | |
| Inhibit protein synthesis | EEF2 | −0.005 |
| EEF2K | −0.394 | |
| Growth arrest | ELAVL1 | −0.252 |
| CCNA1 | 2.574 | |
| CCNA2 | 0.143 | |
| Activated mitochondrial biogenesis | SLC2A4 | 6.386 |
| PPARGC1A | 4.842 | |
| Increased FFA oxidation | CPT1A | −0.260 |
| CPT1B | 0.496 | |
| CPT1C | 0.608 | |
| Gluconeogenesis and glucolysis | ALDOA | −0.106 |
| ALDOB | −1.659 | |
| ALDOC | −0.266 | |
| PFKP | −0.461 | |
| GPI | −0.940 | |
| Fructose-1,6-Biphosphate | FBP | −0.792 |
| NO production | NOS1AP | 0.386 |
| JNK/P38 MAPK | MAPK8 (JNK) | 0.544 |
| MAPK9 (JNK) | −0.266 | |
| MAPK10 (JNK) | 1.492 | |
| MAPK12 (P38) | −0.905 | |
| MAPK13 (P38) | 3.294 | |
| MAPK14 (P38) | −0.848 | |
| Transcription factors | C-JUN (AP1) | 0.795 |
| NFKB | 2.676 | |
| CREB1 | 0.782 | |
| ATF4 (creb TF) | 0.968 | |
| CEBPB (CEBP) | 0.586 | |
| Iron metabolism and/or anti-inflammatory | HMOX1 | −2.686 |
| NRF-2 | 0.855 | |
| P53 | TP53 | −0.554 |
| MDM4 | 3.489 | |
| Toll-like receptor 4 | TLR4 | 0.807 |
| LY96 (MD-2) | 1.213 | |
| LBP | 4.472 | |
| NF-kB signaling and inflammation | RELB | 1.503 |
| NFKB | 2.676 | |
| NFKBIA | 2.578 | |
| NFKB1 (p50) | 2.569 | |
| RELA (p65) | −0.031 | |
| PTGS2 | 5.166 | |
| TNF | 4.990 | |
| PTGS2 | 5.166 | |
| IL8 | 4.779 | |
| IL1B | 7.578 | |
| TNFAIP3 | 2.628 | |
| Lymphoid-tissue homing | CCL21 | 18.917 |
| CCL19 | 5.439 | |
| Myeloiesis and B-cell lymphopoiesis | CXCL12 (SDF-1alpha) | −0.545 |
| B-cell development and survival | TNFSF13B (BAFF) | 2.562 |
| Lymphocyte adhesion, T-cell costimulation | ICAM-1 | 4.055 |
| Initiators of the JAK-Stat pathway (JAK) | JAK1 | 0.213 |
| JAK2 | 2.289 | |
| JAK3 | 2.965 | |
| TYK2 | 0.948 | |
| STAT genes | STAT1 | −0.136 |
| STAT2 | 1.276 | |
| STAT3 | 0.660 | |
| STAT5A | 3.365 | |
| STAT5B | 1.554 | |
| Growth, proliferation, fate determination, development, immunity | IRF9 (p48) | 0.407 |
| PIM1 | 3.108 | |
| EP300 (CBP) | 0.784 | |
| CREBBP (CBP) | 0.881 | |
| CISH (CIS) | 7.170 | |
| Fractalkine/CX3CR1 axis and biological signature of microglial cells | CX3CR1 | 2.017 |
| CX3CL1 | 0.618 | |
| ITGAM (CD11b) | 0.13 | |
| IL1B | 7.578 | |
| Potential epigenetic regulator | HDAC1 | 2.271 |
| LRP phagocytosis signalling | LRP1B | 4.522 |
| LRP2 | 4.860 | |
| LRP6 | 1.052 | |
| Quality Control | TGFBR1 | 0.327 |
| TGFβ | −0.419 | |
| GFAP | −1.044 | |
| ITGAM (CD11b) | 0.130 | |
| CD40 | 4.656 | |
| IBA1 (AIF1) | 0.060 |
*
Bold values correspond to significant log2 fold change (padj < 0.1).