Fig. 6

Expression dynamics of differentially-expressed TEs (DETEs) correlate with that of the co-localised differentially-expressed genes (DEGs). a, b Heatmaps showing hierarchical clustering of DETEs in Vv_Mock vs Vv_T = 0 (a), and DETEs in Vv_Yeast vs Vv_Mock (b), based on logarithmic-transformed fold-changes. The three replicates of each time point are individually presented. The time-series expression pattern of each cluster is depicted as line graph with the number of TE loci within each cluster indicated. c, e Pie charts to summarise the expression pattern of DETEs in Vv_Mock vs Vv_T = 0 (c) and DETEs in Vv_Yeast vs Vv_Mock (e). d, f Hierarchical classification of DETEs in Vv_Mock vs Vv_T = 0 (d) and DETEs in Vv_Yeast vs Vv_Mock (f) by the presence/absence of co-localised genes (genic/intergenic), the transcriptional activity of co-localised genes (with expr. Gene/with non-expr. gene), and the differential test of expressed genes (with DEG/with non-DEG). g, h Heatmaps showing hierarchical clustering of co-localised DETEs and DEGs in Vv_Mock vs Vv_T = 0 (g), and DETEs in Vv_Yeast vs Vv_Mock (h), based on logarithmic-transformed fold-changes. i, j Donut graphs to summarise the hierarchical clustering of co-localised DETEs and DEGs in Vv_Mock vs Vv_T = 0 (i) and DETEs in Vv_Yeast vs Vv_Mock (j) by expression pattern