Figure 4

Transcriptomic analysis reveals altered expression of genes involved in phototransduction

(A1) Heatmap of expression of differentially expressed genes (DEGs) from control and elipsa 4dpf whole larvae (n = 4 RNA preparation obtained from circa 30 elipsa and sibling controls) shown as Z score of log2-normalized read counts. Increased expression is represented with red and decreased expression with blue. A total of 702 (220 upregulated and 482 downregulated) DEGs were identified based on a threshold of p-value adjusted of 0.1.

(A2) Volcano plot showing the DEGs in elipsa as compared with control. The horizontal dotted line indicates the adjusted p-value of 0.1. The vertical dotted line separate upregulated (red) and downregulated (blue) DEGs.

(B) Top 20 Gene Ontology (GO) biological process (B1) cellular component (B2) and molecular function (B3). Genes associated with GO terms related to phototransduction (magenta), cilia (blue) and neuronal process (green) are represented in (C1–C3).

(C) Heatmaps showing expression of DEGs (represented as Z score of log2-normalized read counts) associated with (C1) photoreceptor and light detection GO terms (magenta highlights in B1-B3), (C2) cilia GO terms (blue highlights in B1-B2), (C3) neuronal process (green highlight in B1-B2), and (C4) hedgehog signaling (receptors smo and ptch1-2 and transcription factors gli1-3). Red highlights show genes associated with motile cilia function in (C2) and genes of interest in (C3).

See also Figure S3, Tables S1 and S2.