Fig. 4: MuTrans scrutinizes the cellular bifurcation and gene expression dynamics during iPSC differentiation.

a The schematic development landscape during iPSCs differentiation, with cell states and lineage relationship inferred by MuTrans. EPI: epiblast cells. PS: primitive-streak cells. En: endodermal cells. M: mesenchymal cells. b, c The multi-scale quantities learned by MuTrans. b The learned cellular random walk transition probability matrix (rwTPM). Elements in red circle indicate that cell-cluster scale rwTPM recovers the finer resolution of cell-cell scale rwTPM than the cluster-cluster scale rwTPM. c The cell-cluster assignment, cluster-cluster transition probability and cell-cluster membership matrix learned by MuTrans. d MuTrans outputs shown in UMAP dimension reduction plot, including attractor basins, transition entropy of each cell and gene expression values of endodermal (En) marker Sox17 and mesodermal (M) marker Hand1. e The transition path analysis by setting epiblast (EPI) attractor as start state and the mesodermal (M) attractor as target state, overlaid on the two-dimensional dynamical manifold. The numbers indicate the relative likelihood of each transition path. The cells are colored by MuTrans attractors. The grayness indicates energy values of dynamical manifold, with darker colors representing lower energy values. f The violin plot of transition entropy distributions grouped and colored by different cell collection time points (days). g The constructed dynamical manifold. The color of each individual cell is computed based on the value of its soft clustering membership. h The Transcendental analysis of the transition from Pre-M state to M-state. The TCS (transition cell score) are shown with transition cells marked by dashed rectangles. Transition cells are marked by dashed squares. The average gene expression of top 5 MS (meta-stable genes, blue), IH (intermediate-hybrid genes, yellow) and TD (transition-driver genes, green) are displayed over the ordered cells in transitions. The full gene name list is shown in Supplementary Table 4. The thin lines represent the raw normalized expression value and thick lines denote the smoothed data. i GO (gene ontology) enrichment analysis of MS, IH and TD genes during Pre-M to M state transition indicates a gradual loss of endodermal property and gain of mesodermal property in the cell-fate switch.