Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
Figure 3
Differentiation and reprogramming process represented by 313 nodes (every node denotes a cell state, characterized by expression patterns of the 22 marker genes) and 329 edges (paths).
The sizes of nodes and edges are proportional to the occurrence probability of the corresponding states and paths, respectively. Red nodes represent states which are closer to stem cell states in terms of gene expression pattern, and blue nodes represent states which are closer to differentiation states. The green and magenta paths denote dominant kinetic paths from path integral separately for differentiation and reprogramming. Here, we set a probability cutoff to decrease the number of states and paths, i.e. we only demonstrate the states and paths with higher probability. The largest red node (high NANOG/low GATA6/low CDX2) represents most major ES state (stem cell state), and the largest blue node (low NANOG/high GATA6/high CDX2) represents most major differentiation state. IM1 represents a intermediate state (low NANOG/low GATA6/low CDX2), and IM2 represents another intermediate state (high NANOG/high GATA6/high CDX2).