Comparison of RPKM of each gene after pathogen infection. RPKM (Reads Per Kilobase of exon model per Million mapped reads) values for Phytozome annotated transcripts (left) or novel Cufflinks-predicted transcripts (right) were compared in mock-infected (control) and pathogen-infected leaves. For each gene, the RPKM (log2) value in mock-infected plants is plotted on the horizontal axis and the corresponding RPKM (log2) value in pathogen-infected plants is plotted on the vertical axis. Distributions of the number of transcripts are given as colors. A constant of 0.01 was added to each RPKM to avoid zero scores in log calculations.