Fig. 1

The two pivotal foci of this study: the time axis and the effect of HGF. A Schematics illustrating the scopes of the comparative analyses. Suematsu et al. provided an overview of the effect of HGF across a time series (left). To explore its dynamics along the time axis, we conducted “multidimensional” comparisons. First, we identified upregulated (or downregulated) genes in terms of the comparative factor (X) and quantified the overlaps of those genes with the other factor (Y) using Venn diagrams. This procedure enabled us to visualize the degree of similarity (or difference) in terms of X between the two series that are different in Y. We measured the overlap of timewise upregulation/downregulation between HGF + and control samples to juxtapose their timewise trajectories (center) and the overlap of gene regulation driven by HGF on Days 2 and 7 to visualize the temporal shifts in the HGF effect (right). B Conceptual schematic for the temporal variation in the effect of HGF. In addition to some time-consistent effects (denoted as continuous effects), effects that appear temporarily in the early stages (denoted as early effects) and effects that surge in the later stages (denoted as delayed effects) can be considered. C Overview of the dataset: The marker colors reflect the status of HGF administration, while the marker shapes indicate the time points. Each axis is a PC with a labeled contribution rate. D Scatter plots of genes (horizontal axis: Cohen’s d values; vertical axis: PC1 components) for HGF + (top) and control (bottom) rats. We defined the upregulated genes as those with a Cohen’s d > 0.8 and the downregulated genes as those with a value < 0.8. Note that the upregulated genes were enriched in Day 7 samples, and the vertical axis was not related to gene selection (for visualization purposes only). E Scatter plots of genes (horizontal axis: Cohen’s d values; vertical axis: PC2 components) for Day 2 (top) and Day 7 (bottom). The same definitions of the upregulated/downregulated genes as in (D) were applied. Note that the upregulated genes were enriched in HGF + samples, and the vertical axis was for visualization purpose only