Figure 3: Enrichment analyses of the 595 genes differentially expressed in the roots during an inductive 22-h LD.

(a) Tissue enrichment. For each gene, expression was localized in the tissue where Brady et al.²⁵ found highest transcript level. In each tissue, the number of differentially expressed genes is indicated in bold whereas the number of genes that would be expected for this dataset is enclosed within brackets. Shaded area shows p-values >0.01. Over- and under-represented genes are separated by the horizontal dashed red line. (b) Gene ontology term enrichment in the list of 595 differentially expressed genes. GO identifiers are enclosed in brackets. The number of differentially expressed genes experimentally associated with each term is indicated in bold, whereas the number of genes associated with the GO term that would be expected by chance for this dataset is enclosed within brackets. Bars indicate the −log₁₀(p-value) for each term (Fisher’s exact test). (c) Motif enrichment analysis in the −500 to +50 nt region of the genes that were down- or up-regulated at h16 or at h22 in LD. Numbers are the p-values of motifs that were identified as enriched by AME at p < 0.05 in any of the 4 differentially expressed gene subsets. / indicates non-enriched motif.