Figure 2

Figure 2 Expression profiling reveals pathways downstream of Opn4

A   Representation of the zebrafish adult brain shows the lateral and dorsal view with abbreviations for the following domains: olfactory bulb [OB], telencephalon [Tel], epiphysis cerebri or pineal [E], optic tectum [TeO], cerebellum [Ce], medulla oblongata [MO], hypothalamus [H] and hypophysis or pituitary [Pit]. Transcriptome sequencing was performed on cDNA from wild‐type and opn4 dko eyes and brains, sampled in the light phase (ZT4‐6). The brains were separated in an anterior part, which includes part of the forebrain and the pineal, and a posterior part, which includes part of the forebrain and the whole mid‐ and hindbrain. The cut lines through the depicted brain indicate where the brain was partitioned and which parts were subjected to transcriptome sequencing. The blue (anterior brain) and grey (posterior brain) arrows connect the brain parts in (A) with the differentially expressed genes in (B).

B  Venn diagram shows the number of differentially expressed genes in the opn4 dko anterior brain (dark blue circle), posterior brain (grey circle) and eye (light blue circle). The cutoff for differential expression was set at the significance level of α = 0.05. Heat maps of all the differentially expressed genes are presented in Appendix Fig S1A–C. The number of differentially expressed genes that are shared between the data sets is indicated where the datasets overlap.

C   Fisher's exact test shows that the shared differentially expressed genes between data sets are unlikely to be the result of coincidence. P‐values for the common differentially expressed genes are indicated where the datasets overlap. The large number of common differentially expressed genes between the data sets derived from the anterior and posterior brain parts is likely due to forebrain regions that are shared between these parts.

D   Pie chart shows the number of differentially expressed genes in the opn4 dko anterior brain that were assigned with KEGG software to phototransduction (dark blue), metabolic (orange) and other pathways. Of the metabolic pathway, 5 genes were assigned to the subcategory tryptophan metabolism (red), which encode all the enzymes that convert tryptophan into melatonin. Note that 189 genes were not assigned to a pathway.

E   Ancestor charts show the gene ontology attributes to which the differentially expressed genes in the opn4 dko anterior brain were assigned with FuncAssociate software (cutoff: α = 0.05). The number of genes assigned to an attribute is indicated in the upper right corner. All retrieved biological processes and molecular functions are associated with light, consistent with knockout of a photoreceptor.

Source data are available online for this figure.