Table 1.
Reads number based on the RNA-Seq data in two libraries of A. thaliana wild-type (Col-0) under exogenous myo-inositol (MI+ or MI-).
Table 2.
Distribution of all 21868 genes detected in Arabidopsis with exogenous MI treatments via RNA-Seq technology.
Fig 1.
A volcano plot is a scatter plot that is often used when analyzing micro-array data sets to provide an overview of interesting genes. The log2 (FC) (fold change) is plotted on the x-axis, and the negative log10 (FDR) (p-value) is plotted on the y-axis. The red point shows no differential gene expression with the absolute value of log2 (FC) less than 1 (FC = 2) and FDR no less than 0.05. The blue point show differentially expressed genes with the absolute value of log2 (FC) no less than 1 (FC = 2) and FDR less than 0.05.
Table 3.
All 183 DEGs were divided according to the folds of FPKM value between two treatments.
Fig 2.
Hierarchical cluster analyses of gene expression based on log ratio RPKM data.
The cluster display expression patterns for a subset of DEGs in two comparisons (A1-vs-A2) between two treatments. The color key represents RPKM normalized log10 transformed counts. Red represents high expression, green represents a low expression. Each column represents an experimental condition, and each row represents a gene. The columns are evenly divided into three groups, I, II and III. Each group contains 61 genes, their order are arranged in accordance with the blue arrow direction. The green box contains 26 genes, which represented the green rows in III group.
Fig 3.
The results are summarized in three main categories: biological processes, molecular functions and cellular components by GO analysis. (A) GO classifications of all genes between the two treatments and all 177 DEGs between the two treatments. (B) GO analysis of the down-regulated genes in A1-vs-A2. (C) GO analysis of the up-regulated genes in A1-vs-A2.
Fig 4.
MapMan overview of cellular function (A) and biotic stress (B) showing all DEGs between the two treatments with exogenous myo-inositol.
The big grey circle is an illustrated map of nucleus. The small grey circle indicate annotated biological process (metabolites). The small squares represent individual genes. The color key represents RPKM normalized log2 transformed counts. Red represents up-regulation and blue represents down-regulation between two treatments with exogenous myo-inositol.
Fig 5.
qRT–PCR validation of RNA-Seq results.
Fifteen genes were randomly selected from the DEGs (red columns) from the RNA-Seq data and were analyzed for differential expression changes (blue columns) of the genes. The results were the average of two biological replicate samples in triplicate. Error bars indicate the standard error of two biological replicates in qRT–PCR.