Fig. 2.

Transcriptomic profiling of FZD3 knockdown in human melanoma reveals its pleotropic control of tumorigenic properties. RNA-Seq data using two biological replicates for each shFZD3 and shSC generated melanoma cell lines. (A) PCA of FZD3 knockdown (blue) vs. control specimens (red) shows uniform shift of transcriptional profiles. (B) Hierarchical cluster analysis using correlation distance of log-transformed, normalized FPKM RNA-Seq values of melanoma specimens in combination with knockdown of FZD3. Transcriptomic impact of FZD3 relates to 71.9% of gene activation (down in the melanoma specimens with shRNA knockdown of FZD3, red cluster), and 28.1% of transcriptional down-regulation (blue cluster). Both fractions are equally important, contributing to rewiring of signaling pathways in FZD3-activated melanoma. (C) Pathway enrichment analysis identifies major networks of cell cycle (red), transcription factor networks (purple), MAPK signaling (cyan), and cytokine interactions (blue). (D) Upstream regulator analysis shows hierarchical structure of regulatory network of FZD3. Transcription factor networks of FOXD1, CREB5, and ATF3 (purple) control activity of MAPK effectors (cyan). E2F, MYC, and AP1 targets, and cell cycle (red) are strongly engaged as downstream effectors resulting in a robust proliferative phenotype.