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Fig. 3 | Journal of Experimental & Clinical Cancer Research

Fig. 3

From: Molecular features and vulnerabilities of recurrent chordomas

Fig. 3

U-CH11 and U-CH11R present distinct transcriptomic profiles representative for sacral primary and recurrent chordoma lines. a Volcano plot showing statistical significance (−log10p-value) versus fold change (log2FC) of microarray gene expression data from U-CH11R (n = 3) versus U-CH11 (n = 2). The top five diminished (blue) and enhanced (red) genes in U-CH11R are annotated. Cnetplots illustrating the top three enriched GO-terms and the associated genes of the enhanced (b) and diminished (c) genes in U-CH11R. The fold change of gene expression is indicated by the color, the size of each node represents the number of linked genes to each term. d Rank-rank hypergeometric overlap (RRHO) heatmap for matched and unmatched dataset comparison used to identify significantly concordant transcriptional profiles from two independently conducted microarray gene expression analyses. RRHO was applied to the matched and unmatched data of primary and recurrent chordoma cell lines revealing high overlap between both datasets. The -log10 transformed hypergeometric p-value indicates the strength of enrichment (refer to legend). Concordantly up- and downregulated genes are located in A and D, respectively, disconcordantly expressed genes are in B and C. e Gene set enrichment analysis of the concordantly upregulated genes in recurrent chordoma cell lines. The top six enriched GO-terms and associated genes are given

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