Figure 1.
Number of unique and common differentially expressed genes (DEGs) found in rice and Arabidopsis.
The number of orthologous genes found between rice and Arabidopsis DEGs are also shown. RD: Rice Drought, RB: Rice Bacteria, AD: Arabidopsis Drought, AB: Arabidopsis Bacteria.
Figure 2.
Summary of significant GO terms found in different stresses.
Terms in green arrow indicate those that are commonly upregulated in drought and bacterial stress, and the terms besides the green arrow indicate those that are specifically upregulated in one stress. Similarly the terms in red arrow and those besides indicate the terms that are downregulated in both stresses and specific to one stress respectively. Terms in yellow oval were found both in up and downregulated gene sets. The terms in bold and those in italics are highly significantly found in rice and Arabidopsis respectively. B.P: Biological Process, M.F: Molecular Function, C.C: Cellular Component.
Figure 3.
Dendrograms and heatmaps of SRGs divided into tightly co-expressed modules by the R statistical package WGCNA.
A) RB, B) RD, C) AB, and D) AD. The DEGs were clustered based on co-expression patterns as represented by the dendrogram and correlation heat map. Clusters of like-regulated genes are referred to as modules and are indicated by different colors. Grey color represents the genes that could not be assigned to a module. Intensity of red coloring in the heat map indicates strength of correlation between pairs of genes on a linear scale.
Figure 4.
Heatmaps of turquoise and blue modules in rice under drought stress.
The x-axis represents microarray samples grouped into drought treated and control samples and y-axis represents genes found in the module. Below the heatmap the corresponding module eigengene expression values are shown. The most significant functional terms found in the module are also shown. The number of genes found in each module and the percentage of up and downregulated genes in each module are shown as a pie chart.
Figure 5.
Clustering dendrogram of genes and consensus modules found in A) rice and B) Arabidopsis.
The correspondence between consensus modules and modules found individually in drought and bacterial stress based on the expression values of the common genes are also shown as a table. Each row of the table corresponds to individual stress specific module (labeled by color as well as text along with the number of genes in the module), and each column corresponds to one consensus module. Numbers in the table indicate gene counts in the intersection of the corresponding modules. Coloring of the table encodes -log(p), with p being the Fisher's exact test p-value for the overlap of the two modules. The stronger red color indicates more significant overlap.
Figure 6.
Gene expression profile of rice consensus module magenta under fungal and salt stresses using the tool Genevestigator.
The heatmap shows color coded values based on Log(2)-ratio of test/control samples in different studies. A brief description of test/control samples including tissue, treatment and cultivar is also given. The top TF gene WRKY47 (LOC_Os07g48260) is highlighted with a red box and the corresponding log(2)-ratio, fold change and p-values across different microarray studies are shown.
Figure 7.
Coexpression network of SRGs common to drought and bacterial stresses.
(A) rice (B) Arabidopsis. Nodes are color coded based on consensus modules found by WGCNA. Edges are constructed between genes with correlation coefficient (r) >0.8. The edges with r >0.8 are show in red. The gene IDs, description and number of edges of top 2 nodes in each of the networks are shown in green colored boxes.