Fig. 2

Transcriptome dynamics in response to LCOs. A ESCAROLE results for seven modules, based on transcript abundance data. Each heatmap includes genes assigned to that module at that time point, and the height of each heatmap corresponds to the number of genes (inset numbers). B The module assignment heatmap depicting typical gene expression trends obtained by hierarchical clustering of gene module profiles into transitioning gene sets. Shown are the mean module assignments, number of genes in each set, and expression levels at each time point for each cluster. Arrows indicate two example trends of expression change. C Examples of transitioning gene sets showing gene expression upregulation or downregulation, enriched for genes implicated in nodulation such as defense response to bacterium (cluster 293) and meristem growth (cluster 186)