Figure 1.
Transcriptome age index (TAI) using raw and log-transformed expression signal intensities.
A higher TAI value implies that evolutionary younger genes are preferentially expressed at the corresponding time-point. The pink shaded area indicates the phylotypic stage. Colors of the curves reflect the main developmental periods and correspond to the colors used in [11].
Figure 2.
Modules of genes with time-specific expression during zebrafish development.
A) Zebrafish ontogeny (drawings of the embryos are based upon sketches and photographs from [49]. B) Median, 25th and 75th percentiles of expression value of genes in modules. Red bars denote the condition scores assigned to developmental points by the ISA.
Figure 3.
Measures of developmental constraints for various gene properties.
A) Box and Whisker plot showing non-synonymous to synonymous substitution ratios () for genes in the modules. The dotted line denotes median
for all genes. The dash-dotted lines denote confidence interval for the median. B) Observed minus expected frequencies of age of genes in modules. C) Observed minus expected frequencies of orthology type (between zebrafish and mouse) for genes in modules. D) Mean expression level of zebrafish genes in modules, and their one-to-one orthologs in mouse in six developmental metastages. The transition between the two mouse data sets is denoted with the vertical dashed line. The Pearson's correlation coefficients for zebrafish and mouse expression profiles are reported for every module. E) The number of transcription factors (TFs) in modules (whole bar) and their enrichment in highly conserved non-coding elements (HCNEs) and transposon-free regions (TFRs). The stars denote significant enrichment (
) of TFs in HCNEs (yellow) and in TFRs (red). The dash-dotted lines denote confidence interval for the expected number of TFs in modules.
Figure 4.
Mean expression level of zebrafish genes in modules, and of their one-to-one orthologs in mouse. The same colors denote corresponding developmental metastages in zebrafish and mouse.