Figure 5.
Combinatorial rather than hierarchical TF expression and regulation in the mesoderm
(A) Identification of genes specifically associated with one of the major cell type transitions during gastrulation. Shown are relative expression levels of genes, comparing between the source cell population and its progeny (columns). Dashed boxes mark the enriched, early-specialized lineages. Selection criteria for genes: (1) minimal gap of 0.5 between largest and second-largest log fold-change along a transition, and (2) second-largest fold-change smaller than 1.
(B) Absolute expression of highly variable TFs in the mesoderm. Columns represent individual MCs following hierarchical clustering.
(C) Temporal expression of key TFs within the mesoderm. For each TF, we identified the MCs with maximum expression in the mesoderm (see STAR Methods). The inferred TF expression kinetics along trajectories leading to such MCs are shown. Error bars reflect SD of expression for traced-back MCs at each time point. y axis, absolute expression.
(D) R2 values for the best regression model using a pair of mesodermal TFs versus the best model using only one TF, trained on non-TFs with the highest variance in the mesoderm, and validated using permutation tests (see Figure S5).
(E and F) Prominent examples of target genes that can be accurately fitted in the mesoderm (R2 > 0.8) using a single TF (E) or a linear combination of two TFs (F). Each dot represents a MC, axes represent absolute expression of TFs and predicted gene (x and y, respectively).