Fig. 5
From: SMARCB1 orchestrates cellular plasticity and oncogenic pathways in typical and chondroid chordomas
Transcriptome analysis reveals SMARCB1-associated pathways in chordoma. (A) Principal Component Analysis (PCA) plot showing distinct clustering of SMARCB1-high (negative, red) and SMARCB1-low (positive, blue) chordoma samples. PC1 explains 72.7% of the total variance. (B) Volcano plot of differentially expressed genes between SMARCB1-high and SMARCB1-low samples. Blue dots represent significantly down-regulated genes, red dots represent significantly uP-regulated genes (log2 fold change cutoff: 1, P-value cutoff: 0.05). (C) Gene Set Enrichment Analysis (GSEA) of hallmark gene sets, showing significant enrichment of MYC targets, E2F targets, and G2M checkpoint pathways in SMARCB1-low samples. NES: Normalized Enrichment Score. (D) GSEA of Gene Ontology (GO) Biological Process terms, highlighting enrichment of cell cycle-related processes and negative enrichment of cellular adhesion processes in SMARCB1-low samples. (E) GSEA of KEGG pathways, demonstrating enrichment of DNA replication and cell cycle pathways, and negative enrichment of tight junction and adherens junction pathways in SMARCB1-low samples. (C–E) The running enrichment score for each gene set is shown at the top of each panel, and the vertical bars below represent individual genes in the gene set, colored by their correlation with the SMARCB1-low phenotype (red: positive, blue: negative).
