Figure 3
From: A stochastic model dissects cell states in biological transition processes
A stochastic, multi-state model for reprogramming.
(a), We fitted a four-state model to gene expression time-course data from a secondary MEF-based reprogramming system due to Samavarchi-Tehrani et al.18. (b), Estimated rates for each transition. (c), The probability of a cell to be in a particular state as a function of time during reprogramming. (d), Observed time-course data (blue with crosses) and output of the fitted model (green) for selected genes. (e), Genome-wide, state-specific gene expression signatures. The cell states have markedly different global transcriptional profiles. (f), Gene expression signatures for selected genes that are discussed in the text. Red genes have state-specific expression that is below and green genes above the state average (dotted vertical lines). Genes are shown by category, from top to bottom: pluripotency, epithelial, signaling, mesenchymal and growth. The model highlights major transcriptional changes between states, including a mesenchymal-to-epithelial transition from state 2 to 3 and the establishment of pluripotency marker genes in the transition from state 3 to 4.
