Figure 4

Common abiotic stress regulons in Arabidopsis Col-0. (A) Gene co-expression network visualizing the 20 largest modules at the first and second levels of organisation. Modules are colored by significantly enriched gene-sets according to a hypergeometric test. For modules with more than one color, more than one gene-set was significant. (B) Overlaps between sets of significantly upregulated (UP) or downregulated (DOWN) transcripts in Col-0 wild type at early (EARLY stress regulons) and late time-points (LATE stress regulons). (C) Gene ontology (GO) and KEGG pathway enrichment analysis of the EARLY and LATE UP and DOWN stress regulons. The size of the circle and color intensity indicates the significance (−log p-value (Benjamini-Hochberg adjusted)) of the enrichment for each functional category. Numbers beside each circle indicate the number of genes attributed to each category that are present in each regulon. The total number of genes from each GO category in Arabidopsis thaliana, which were present in our detected population, is shown in parentheses after their GO consortium or KEGG pathway ID. Some redundant functional categories were excluded for clarity.