Table 1.
Top enriched pathways among DEGs of major cell types (FDR<5%) and representative DEGs in the select pathways
| Cell type | No. DEGs | Top DEG pathways | Top 5 representative DEGs |
|---|---|---|---|
| Astrocytes | 247 | Metabolic depression | Down: Mdh1,Atp5b,Cox4i1,Atp5a1,Ndufs7 |
| Calcium/calmodulin pathways | Up: S100a11,Syt1; Down: Calm1,Calm2,Camk4 | ||
| Microglia | 57 | Inflammation/immune response | Up: Cebpb,Il1b,Cxcl1; Down: Selplg,Cx3cr1 |
| Oligodendrocytes | 115 | Myelination | Up: Klk6; Down: Mbp,Mal,Sirt2,Tspan2 |
| Oligodendrocyte differentiation | Up: Sox10; Down: Gstp1,Cnp,Tspan2,Olig1 | ||
| (Oligodendrocyte PCs) | 7 (103) | Myelination | Down: Mbp,Plp1,Sirt2,Mag |
| Immune response | Up: Prkx; Down: Egr1,Fyn | ||
| Endothelial | 35 | Amyloids | Up: Ttr,B2m; Down: Itm2a,Itm2b |
| (Ependymal) | 87 (783) | Cilia related pathways | Down: Tmem107,Ift43,Dynll1,Spag17,Spef2 |
| Platelet degranulation | Up: Igf2; Down: Rarres2,Scg3,Clu,Pros1 | ||
| Amyloids | Up: Cst3; Down: Itm2c,Apoe,Bace2,Apbb1 | ||
| (Unknown1) | 1 (52) | Dendrite morphogenesis | Down: Epha4,Stk11,Baiap2,Bhlhb9 |
| Neurons—general | 139 | Neurogenesis | Up: Npy,Inhba,Adgrl3; Down: Ndn,Cck |
| Energy-related | Up: Atp1a1,Atp1a2,Atp2b2; Down:Atp1b1 | ||
| Synaptic signaling | Up: Scn1b,Cplx2,Slc17a7,Grik4,Grin2b | ||
| (CA1 neurons) | 16 (330) | Glutamate transport | Up: Slc17a7,Grin2b,Gria1,Gria2 |
| Metabolic depression | Down: Ndufa4,Atp5d,Atp5g1,Ndufv3,Cox8a | ||
| (CA3 neurons) | 14 (209) | Biosynthesis | Up: Ncan; Down: Mrpl57,Eef1a2,Farsb,Rpl15 |
| (CA subtype1 neurons) | 6 (204) | Neurotransmitter pathways | Up: Camk2a,Ppp1r1b,Grin2b,Cav2,Prkcg |
| (Neuronal subtype2) | 11 (139) | Proteosome | Up: Rpn1,Psmc6,Psma1 |
| DG granule cells | 44 | Neuroplasticity/neurotropic | Up: Set,Bdnf; Down: Chl1,Ntf3,Pcp4 |
| Cell-cell signaling | Up: Ptprn,Penk,Npy,Inhba,Pcdh8 | ||
| (GABAergic interneurons) | 6 (240) | Cell migration | Up: Wasl,Arpc3,Pik3ca |
DEGs listed as up had increased expression in TBI and DEGs listed as down had decreased expression in TBI compared to sham. Cell types shown in parenthesis are rare cell types with fewer cells analyzed, and hence did not have sufficient numbers of DEGs at FDR < 5% between Sham and TBI samples to reveal significant pathways. Instead, DEGs reaching a threshold of p < 0.01 (number of DEGs shown in parenthesis) were used to derive suggestive pathways for these rare cell types. P values were determined using a bimodal likelihood ratio test