Figure 5.
Continue training on the time-course RGC ONC dataset
(A) UMAP visualization of the control group (0 dpc) RGCs.
(B) Initial prediction accuracy at different time points when applying models trained on the previous time point data. For each time point, accuracies are shown for overall predictions (yellow), certain predictions (green), and ambiguous predictions (orange).
(C) Comparison of prediction accuracy for ambiguous cells only, before and after continued training. “First Apply” shows the accuracy of ambiguous predictions from the initial model application (orange bars in [B]). “Cont. Training” shows improved accuracy for these same ambiguous cells after training the model for an additional 30 epochs on cells with certain predictions.
(D) UMAP visualization of later time points at 4 dpc (left), 7 dpc (middle), and 14 dpc (right). Cells with certain predictions from both the initial application and after continued training are plotted to visualize the results. The prototypes are represented by dots with black edges. Cell types are ordered by injury survival, from the most resilient (C43) to the most susceptible (C28), with an increasing proportion of unassigned cells after 4 dpc.
(E and F) (E) HRG expression of T5-RGCs at 4 dpc and (F) 7 dpc. Comparison of top-ranked HRGs and differentially ranked HRGs between C1 RGCs and other T5 RGCs. “C1 specific” are highly ranked HRGs within C1 (rank < 30) with low relevance in other types (mean rank > 200). “C1 diff HRG” represents genes with the opposite pattern. Re-assigned “unassigned” cells predicted as C1 are included with “Pred_C1.” “Marker” refers to known canonical markers for each cell type based on established literature.53 Genes include known markers (Tusc5 shared by all T5 RGCs, Serpine2 and Amigo2, and C1 RGC marker genes), HRGs shared by all T5 RGCs, and differentially ranked HRGs between C1 and other T5 RGCs.
(G and H) (G) HRG expression of ooDSGCs at 0 dpc and (H) 7 dpc, including predicted C10 cells (Pred_C10). Shared and distinct HRGs are compared between C10 and other ooDSGCs, with known markers Gpr88 (a C10 RGC marker) and Fam19a4 (a C24 RGC marker).