Developmental- and stage-specific expression of lincRNAs. (A) Differential expression of lincRNAs. For each lincRNA and mRNA, the maximum RPKM value from 10 distinct developmental stages (Supplemental Table S1B) is plotted relative to the mean value for the remaining nine stages. If the mean value was 0, a small value (0.1) was added to avoid the log 0 value error. For stages with multiple samples, the median value of RPKMs was used. The inset shows cumulative distributions of log2-scaled ratios of maximum and mean RPKMs for lincRNA and mRNAs. (B) Dauer-specific expression of linc-3. Plotted are the RPKM values of linc-3 in 10 distinct stages. (C) Four large lincRNA expression clusters over 35 different developmental stages/conditions (top key). Colored asterisks indicate lincRNA genes within 10 kb of each other. Within each cluster, lincRNAs are sorted based on their expression level (mean RPKM), with the expression level indicated at the far right. The five columns on the right show the abundance (RPKM) of endo-siRNAs mapping antisense to each lincRNA (bottom key). (D) Correlation between lincRNA expression and that of their closest protein-coding gene. Shown is the average correlation for pairs with the indicated relative orientations (tandem, convergent, and divergent), considering only pairs within 1 kb of each other. As a control, mean correlations were also calculated for number-matched cohorts of random pairs of lincRNA and protein-coding genes. For comparison, mean correlations were calculated for number-matched cohorts of protein-coding gene pairs. For both the controls and comparisons, the average correlation of 1000 cohorts is reported for each orientation, with error bars showing the 95% confident interval.
