FIGURE 4

Comparison of the transcriptome profiles of depdc5, tsc2 and double homozygous zebrafish larvae. (A) Spearman’s rank correlation matrix of the RNA-Seq data showing separate clustering of wild-types, depdc5 ^−/−, tsc2 ^−/− , and double homozygous larval samples. Areas of the circles show absolute values of corresponding correlation coefficients. Different genotypes are indicated in distinct color codes. Scale bar indicates the strength of the correlation. (B) Linear and significant relationship between the levels of pS6 protein and the amount of DEGs. (C) Volcano plot showing the differentially expressed genes (DEG) (padj <0.05) between depdc5 ^−/−and wild-type larvae. (D) Volcano plot showing the DEGs (padj <0.05) between tsc2 ^−/− and wild-type larvae. (E) Volcano plot showing the DEGs (padj <0.05) between double homozygotes and wild-type larvae. (F) Overlap of differentially expressed genes between depdc5 ^−/−, tsc2 ^−/− , and double homozygous zebrafish larvae. For the depdc5 ^−/− and tsc2 ^−/− homozygotes 90% and 80% of the total DEGs, respectively, were found to overlap with that of the double homozygotes. The proportion overlapping DEGs with the double mutant were dependent on the genotype of the zebrafish (Chi-squared test, p-value = 3.648e-13). (G) Enriched KEGG pathways from differentially expressed genes between double homozygous zebrafish larvae and wild-types. Pathways enriched amongst upregulated genes are indicated in red, pathways enriched amongst downregulated genes are indicated in blue. The x-axis represents the log10 (1/p-value), n indicates the number of genes appearing in each pathway. (H) GO enrichment map from up and downregulated genes between double homozygous zebrafish larvae and wild-types and (I) tsc2 ^−/− zebrafish larvae and wild-types. Each node represents a different GO term, the red and blue outside of nodes indicate enrichment in up or downregulated genes, respectively. Green node indicating GO term enriched in both up and downregulated gene lists. The larger the node the greater the number of genes in the enriched GO term. Connecting lines indicate common genes shared between nodes, the thicker the line the more genes in common.