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Fig. 3 | Genome Biology

Fig. 3

From: Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

Fig. 3

Transcription factor activity in single cell yeast. TFA estimated from hierarchical SupirFactor model. Violin plots are generated by scaling [0, 1] the underlying measurement. A Cell cycle TFs regulate gene expression in specific cell cycle phases, with the phase the TF regulates annotated on the right y-axis [45]. Cell cycle phase of each cell is inferred from transcriptome and annotated on the x-axis. Panel (i) plots TFA, and panel (ii) plots the RNA expression of the TF. B Same as A. Dot size represents the percentage of cells with a non-zero value. Color represents log fold-change (log FC) across the cell cycle phases. Panel (i) plots TFA, and panel (ii) plots the RNA expression of the TF. C: Interacting TF pair Pearson correlation for SupirFactor TFA, Inferelator TFA, and TF expression. D Comparing TFA between rapamyacin (RAPA) treated and untreated (YPD) cells TFs known to be activated by treatment [46] or known to be more active in untreated cells are annotated on the right y-axis. E UMAP projection of the scY dataset showing TFA estimate of co-regulator TFs and growth conditions

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Genome Biology

ISSN: 1474-760X

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