Fig. 3

Distinct kinetics of gene responses in unc45b mutants. Soft clustering (k = 6) of mis-regulated genes in unc45b−/− embryos at 24 hpf, 48 hpf and 72 hpf in comparison with wild-type embryos. The expression levels were normalized and the y-axes indicate relative expression. The two independent measurements at each of the three time points are aligned along the x-axis of each graph. Genes with high membership after soft clustering are depicted with red lines and those with moderate membership with green lines and low membership with blue lines. Details on GO terms enriched in these clusters are provided in Additional file 6. a Cluster 1 represents genes that are down-regulated in wild-type (WT) siblings from 24–72 hpf. In contrast, these genes are maintained at a constant level in unc45b mutants over the same period. This cluster contains genes with a function in protein folding and maturation. b Cluster 2 genes are expressed at varying levels in 24-, 48- and 72-hpf wild-type siblings while they are maintained at relative constant expression levels in unc45b mutants. Genes in this cluster are associated with GO terms like cytoskeletal proteins in oligodendrocyte development and remodeling and cell adhesion. c Genes of cluster 3 rise moderately in their expression levels in wild-type siblings, while a much more pronounced increase is evident in the RNA samples isolated from unc45b mutants. Gene functions included in this cluster are blood vessel morphogenesis and skeletal muscle development. d Cluster 4 includes mRNAs of genes that are moderately down-regulated in wild-type siblings and increased in unc45b mutants over the three time points. These genes included genes with functions in protein folding. e Cluster 5 represents genes that are up-regulated in both wild-type and unc45b mutant embryos from 24–72 hpf but with a slightly lower slope in the mutant. Genes of this cluster are associated with a range of different GO categories, including cytoskeleton, intermediate filaments, and vesicle transport. f Cluster 6 includes genes that are down-regulated over the analyzed time period in both unc45b mutant and wild-type siblings even though the down-regulation in the mutant was less pronounced. GO terms of this cluster include developmental signaling, regulation of angiogenesis and neurogenesis