Skip to main content
. 2021 Aug 20;12:5056. doi: 10.1038/s41467-021-25326-8

Fig. 4. RNA sequencing of SALL4 knockdown reveals an invasiveness gene expression signature.

Fig. 4

a RNA seq row z-score heatmap of differentially expressed (DE) genes after 48 h SALL4 knockdown in the human cell line M010817. Cutoffs were set at Log2 ratio ≥ 0.27 or ≤−0.27, p value < 0.05 and FDR < 0.05 and resulted in 1004 genes significantly upregulated and 1140 genes significantly downregulated. b Top 12 MetaCoreTM process networks of upregulated genes. Top ten most upregulated genes per process are listed and genes validated in additional cell lines are highlighted in bold. c Top 12 MetaCoreTM process networks of downregulated genes. Top ten most downregulated genes per process are listed and genes validated in additional cell lines are highlighted in bold. d Gene Set Enrichment Analysis (GSEA) of DE genes after SALL4 knockdown (log2 ratio-ranked) as in a with published genesets characterizing invasive versus proliferative melanoma cells40–42. e Log2 expression ratio heatmap of qRT-PCR-based gene expression analysis of specific genes of interest (normalized to PPIA and set relative to siCtrl-treated cells) in human melanoma cell lines (M010817: NRASQ61K; M070302: unknown mutational status; M150548: BRAFV600E; M121224: NRASQ61K and BRAFV600E; MM150536: BRAFV600E) after 48 h treatment with two different siRNAs targeting SALL4. Two-sided t-tests were performed with N = 3 and p values ≥ 0.05 = n.s. Source data for e are provided as a Source Data file.