Thousands of oscillating genes are synchronized with the molting cycle in P. pacificus. (A) The heatmap displays the cross-correlation of log2-transformed expression patterns of all reliably expressed genes (reg; n = 23,135) obtained from the 38 time points. The time course was broken down into seven substages: J2 intermolt (J2_I), J2 molt (J2_M), J3 intermolt (J3_I), J3 molt (J3_M), J4 intermolt (J4_I), J4 molt (J4_M), and young adults (YA). (B) Proportion of variance (PoV) of gene expression by 38 principal components (PCs; left graph) and changes (loadings) of expression for each of the four top PCs (right graph). (C) The heatmaps visualize changes in gene expression throughout development for nonoscillating genes (n = 20,171; left) and oscillating genes (n = 2964; right). The mean TPM was calculated from three biological replicates and was normalized by its maximum of each expression trace. The order of rows in the heatmap with the oscillating genes was sorted by phase class, which indicated a phase difference of 30, corresponding to a peak shift by ∼1 h. (D) Oscillating genes were tested for overrepresentation of protein domains. The left part shows the 17 protein domains that are most significantly enriched among oscillating genes, the x-axis presents the enrichment score, and the y-axis shows the name of protein domains. The size of circles corresponds to the number of oscillatory genes with a given protein domain, and the three different colors indicate significance levels as measured by Fisher's exact test. The right graph profiles the overrepresented protein domains according to the 12 phase classes. The number of oscillatory genes in each phase class is marked.
