A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences
Fig 3
Functional pathways for which cell-to-cell heterogeneity in expression correlates with proliferation rate across cell types and species.
(A) In Gene Set Enrichment Analysis, genes are sorted by their fast/slow expression value (left panel, bottom), and each gene is represented by a single black line (left panel middle). The enrichment score is calculated as follows: for each gene not in the GO preribosome gene set, the value of the green line decreases, and for each gene in the gene set, the value of the green line increases. The ES score will be near zero if the genes in a gene set are randomly distributed across the sorted list of genes, positive if most genes are to the left, and negative if most genes are to the right. (B) The heatmap (right panel) shows the expression (z-scored read counts) of preribosome genes in fibroblasts across four biological replicates of the CFSE sorting experiment. (C) Gene sets enriched (FDR<0.1) in both fibroblasts and ESCs were mapped as a network of gene sets (nodes) related by mutual overlap (edges), where the color (red or blue) indicates if the gene set is more highly expressed in fast (red) or slow (blue) proliferating cells. Node size is proportional to the total number of genes in each set and edge thickness represents the number of overlapping genes between sets. (D) GSEA results (FDR<0.1) of S. cerevisiae [8] that sorted by cell-to-cell heterogeneity in proliferation rate. (E) Pearson correlations of mean expression (average of log2(TPM+1)) of ribosome biogenesis genes vs proteasome genes across organ developmental time courses in seven species (see also S2 Fig).