Deviantly expressed genes (DvEGs)

Genes are “deviantly expressed” (DvEG) in each perturbation, if they are 1) upregulated during a wild-type transition wild-type, but are underexpressed in perturbed cells undergoing that same transition relative to controls or 2) downregulated during a wild-type transition overexpressed in perturbed cells, but are overexpressed in perturbed cells undergoing that same transition relative to controls.

The function calculate_dvegs() takes in the following inputs:

• perturb_degs - output of compare_genes_within_state_graph
• ref_degs - output of compare_genes_over_graph
• sig_p_val_thresh

sig_dvegs = calculate_dvegs(perturb_degs, 
                            ref_degs, 
                            sig_p_val_thresh = 0.05)

We can look for deviantly expressed genes in the pectoral fin in the lmx1b crispant. We first need to run WT and MT degs using compare_genes_over_graph and compare_genes_within_state_graph. For more information on these functions see our DEG page.

pf_graph_degs = compare_genes_over_graph(pf_ccs,
                                         pf_cell_state_graph, 
                                         cores = 4)

perturb_degs = compare_genes_within_state_graph(ccs, 
                                                perturbation_col = "gene_target", 
                                                control_ids = c("ctrl-inj"), 
                                                perturbations = c("lmx1ba,lmx1bb"),
                                                cores = 6)

dvegs = calculate_dvegs(perturb_degs, 
                        pf_graph_degs, 
                        sig_p_val_thresh = 0.05)                                                

The gene col2a1a comes up as a deviantly expressed gene in the pectoral fin condensate. In the wild type it is specifically upregulated, as shown on the Platt graph:

plot_gene_expr(pf_state_graph, genes = c("col2a1a"))

In the lmx1b KO, col2a1a has significantly lower expression in the mutant than in the wild type. We can plot it on the Platt graph:

plot_degs(pf_state_graph, perturb_degs %>% filter(gene_short_name == "col2a1a"))

For more information on how to plotting Platt graphs, see our plotting page.