Fig. 4

An example of negative correlation in expression between an lncRNA and its neighboring PC gene. a The expression of lncRNA XLOC_014500 (red line) and neighboring coding gene XLOC_014501 (black line, gene22438) is negatively correlated. Y-axis shows the expression level by Z-score obtained from averaged FPKM of two replicates. b IGV view of aligned RNA-seq read counts for XLOC_014500 and XLOC_014501 based on two fruit tissue stages: Cortex-1 (pre-fertilization) and Cortex-5 (post-fertilization). The panel of “Reference” shows the gene structure based on genome annotation version1.1. Thin line indicates intron and thick line denotes exon. The panel of “Isoform” shows transcript variants predicted by Cufflinks. The bottom four panels illustrate the RNA-seq read counts in respective tissues. The two replicates are shown with identical color