FIGURE

Fig. 3

ID

ZDB-FIG-230228-419

Publication

Kamimoto et al., 2023 - Dissecting cell identity via network inference and in silico gene perturbation

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Fig. 3

CellOracle KO simulation with zebrafish embryogenesis data.

a, Two-dimensional force-directed graph of the axial mesoderm (AM) sub-branch (n = 1,669 cells) in a published zebrafish embryogenesis atlas (Farrell et al.³²). Arrows indicate notochord cell differentiation (top) and prechordal plate differentiation (bottom). b, Conversion of URD-calculated pseudotime (left) into a 2D pseudotime gradient vector field (right). c, Degree centrality scores were used to rank the top 30 TFs in notochord (left) and prechordal plate (right). Black text denotes TFs. Grey text denotes non-TFs. d, Expression of noto projected onto the axial mesoderm sub-branch. e, Noto KO simulation vector and perturbation scores. f, Markov simulation to estimate cell density in the noto KO sample. The simulation predicted inhibited early notochord differentiation and promotion of prechordal plate differentiation, indicating a potential lineage switch.

Expression Data

Expression Detail

Antibody Labeling

Phenotype Data

Phenotype Detail

Acknowledgments

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