Figure 7

(A) Description of steps involved in the RNA-Seq experiment aimed at identifying genes specifically induced by JAK1-A634D (JAK1^GOF) in zebrafish embryos. After performing standard sample collection and RNA-Seq steps, the main comparison at the analysis stage was between JAK1^WT and JAK1^GOF samples. (B) PCA of 28 and 36 hpf data sets consisting of WT, JAK1^WT, and JAK1^GOF samples. The plots shown contain the first 2 components (PC1, PC2) and identify clear differences between JAK1^GOF samples and JAK1^WT or uninjected samples at 28 hpf. (C) Heatmap of average variance-stabilized gene expression values for IFN-stimulated genes that are present among the genes upregulated by JAK1^GOF in at least 1 stage analyzed (28 and 36 hpf) (58 genes) in all analyzed groups of samples. (D) Reactome Pathway analysis of genes upregulated by JAK1^GOF shows strong enrichment of immunity-related and DNA damage pathways. Gene ratio is the fraction of the genes in a pathway that were present in the input gene list. Gene count and P values associated with a pathway are indicated by the point size and its color. (E) Heatmaps of average variance-stabilized gene expression values for genes associated with the ?immune system process? GO term in all analyzed groups of samples.