Figure 1

Expressional consistency between RNA-Seq and microarray data. A. Detectable genes reported by each technology based on a common filter procedure (See Methods). Venn diagrams of detectable genes are shown 3 experimental conditions (0 µM, 5 µM and 10 µM) respectively, and overlap rates are calculated by dividing number of commonly detectable genes by the union. B. By-group scatter plot depicting the expression profiles of all genes. Log2 transformed FPKM values from RNA-Seq and log2 scaled microarray gene intensities (normalized) are used in the scatterplot. We added 1 to FPKM value before log2 transformation to facilitate calculation. Commonly detected genes are shown in red color while platform exclusive genes are denoted in black. Both Pearson correlation coefficients (PCC) and Spearman correlation coefficients (SCC) were calculated based on all gene entries (except for those not having probe names on the array or RNA-Seq reference genome). C. By-group expressional density histogram for both commonly detectable genes and RNA-Seq specific ones. The x-axis denotes the RNA-Seq FPKM value (log2 scale) distribution and y-axis shows the frequency of genes within each category. Commonly detectable genes are depicted in black while RNA-Seq exclusive genes are shown in grey color.