Transcriptome dynamics during early zebrafish development.

(A) The correlation of global gene expression profiles and number of differentially expressed genes between developmental stages. Gene expression correlations, as indicated by colors in the bottom triangular, were calculated as the Pearson correlation coefficients using the RPKM values of all the detected genes. Differentially expressed genes were defined as genes with statistically significantly different raw read counts (FDR<0.001) and > = 2-fold changes in the RPKM values between two stages, and their numbers are represented by the colors in the upper triangular. Color bars at the bottom and the right side indicate the scale for correlation coefficients and the numbers of differentially expressed genes, respectively. The two squares with bold borders indicate the correlation and number of differentially expressed genes between the two replicates for the 60 hpf stage. (B) Number of genes significantly up-regulated or down-regulated during developmental stage-transitions. (C) Principal component analysis (PCA) about developmentally regulated genes. The graph illustrates the distribution of each development stage in the space of the first three principal components (PCs). (D) The loading coefficients on the first three PCs for each developmental stage. Stage abbreviations on the x-axes in (B) and (D) are as in Figure 1B.