Limited conservation in the dauer related transcriptomes of the two species. (a) Overlap between genes differentially expressed in P. pacificus (green) and C. elegans dauers versus dauer-exit (12 hours) samples. The rectangular boxes represent the entire transcriptome on the array and their area of overlap represents the 1:1 orthologs between the two species, which are represented on both microarrays. The ovals represent the set of differentially expressed genes in each species. 184 orthologous gene pairs are called significantly differentially expressed in both the species, indicating limited conservation (Fisher's exact test p-value = 0.029). A substantial number of non-orthologous, species-specific genes are also differentially expressed in both the species. These gene sets are further analyzed by dividing them into distinct classes which are indicated in blue text (see main text for details) (b) Comparison of log2 expression fold changes for the set of 6,126 1:1 orthologs for the dauer versus dauer-exit comparison. Pearson's correlation coefficient over the entire set of 6,126 orthologs is r = 0.12, and increases to r = 0.29 for the 184 orthologs, which are significantly differentially expressed in both species (FDR corrected p-value < =0 0.05; purple boxes mark the significant orthologs, number per quadrant I - IV: 51 + 51 + 65 + 17 = 184).