Fig. 3: UNAGI reconstructs the temporal dynamics and the underlying gene regulatory networks of cellular dynamics during IPF progression. | Nature Biomedical Engineering

Fig. 3: UNAGI reconstructs the temporal dynamics and the underlying gene regulatory networks of cellular dynamics during IPF progression.

From: A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Fig. 3

a, Dynamics graph of IPF progression within the stromal cell lineage, comprising four tissue fibrosis grades. Each node symbolizes a cell population, coloured according to cell type, and the edges between two nodes depict the progression trajectory across tissue fibrosis grades. Tracks (trajectories), spanning from control to advanced, are named with the specific cell type and the corresponding control cluster ID. b, Gene regulatory networks for the FibAlv-4 track were reconstructed using the iDREM tool. Individual nodes signify a set of genes, and edges connecting two nodes represent gene regulators regulating expression changes. Paths encompassing nodes from control to advanced depict a consistent set of genes showing the same expression changes throughout IPF progression. The enriched pathways associated with gene paths were also provided. c, The temporal regulatory networks for the FibAdv-17 track. d, Line chart of expression of the top dynamic gene candidates on the FibAlv-4 and FibAdv-17 tracks, the top 10 most increasing and the top 10 most decreasing candidate marker genes through the IPF progression. We applied FDR correction in b using the Benjamini–Hochberg (BH) procedure.

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