Fig 1.
Top: Data types integrated to learn the DREM model include general, static interaction data (A) Transcription factor (TF)-gene interaction; (B) miRNA-mRNA interaction; (C) protein-protein interaction (PPI) and condition specific time series data (right): (D) mRNA expression; (E) miRNA expression; (F) Epigenetic data; (G) Proteomics data. The resulting model (H) provides a summary of different gene groups in the experiment, their expression level, their temporal profiles and the regulators (TFs and miRNAs) that control different bifurcation events the. Bottom I: The iDREM representation of the learned DREM model above. Note that this representation removes the actual levels and only provide a schematic view for the paths and splits in the model. The actual expression levels and several other aspects of the model and the data can be interactively viewed by using the various panels available (left).
Fig 2.
iDREM visualization functions.
Top: Expression of a regulator (E2F5) (A) and its targets (B). 2nd row: Expression patterns (similar to the original DREM result, can be viewed from the tool as well) (C) and the regulators for each of these splits (D). 3rd row: Methylation of a regulator (E) and its targets (F). 4th row: Integration with additional browsers for viewing epigenetic data for specific TFs / genes (G) and protein level for specific TFs/proteins (H). 5th row: Intersection of path genes with single cell data (I) and integrated GO functional analysis (J).