Fig. 4.

Reconstructed gene expression profiles for lung and neural development data. Each figure plots the expression profile of a gene along the different paths in the corresponding model. Each image includes the gene name and the cell type it was assigned to by the model (AT1, AT2, cillated and Clara from the lung model and Neuron from the neuron model). (Top row) Known markers for the different cell types. (Second row) Novel markers not identified in the original papers found by the CSHMM assignments. (Third and fourth rows) Comparison of reconstructed profiles using the CSHMM (top) and discrete HMM (bottom). Several genes have a unique path profile using the CSHMM but did not display such profile when using the discrete model