Fig. 2

Principal components analysis (PCA) and gene functional annotation enrichment analysis of the transcriptomes of FISS-derived and skin-derived fibroblast cell cultures. a Bars indicate the percentage of the variance of gene expression level data, across the eight cell culture samples, that is explained by each of the first seven principal components (PCs). Over 70% of the variance is explained, collectively, by principal component 1 (PC1) and principal component 2 (PC2). b PCA loading scores for each of the samples, for PC1 and PC2. Each mark corresponds to a sample, with mark shape indicating the cell type (see legend). Ellipses indicate groupings of fibroblast and sarcoma-derived cells. The ellipse for the fibroblast samples is highly eccentric due to the loading plot marks being nearly collinear within the sample group. c Significant positive functional annotation enrichment scores based on Gene Set Enrichment Analysis (GSEA) of gene-level differential expression log₂(sarcoma cell / fibroblast) values (obtained from cultured cells), using ortholog mapping and human gene functional annotations from the Gene Ontology. Bar magnitude indicates the GSEA normalized enrichment score; each bar significantly differs from zero score with FDR < 0.05. Each positive bar value corresponds to a significant enrichment of genes with the indicated annotation, with positive log₂(sarcoma cell / fibroblast) values, i.e., evidence for upregulation of genes with the indicated function in sarcoma-derived vs. fibroblast-derived cells. d Significant negative functional annotation enrichment scores based on GSEA of gene-level log₂(sarcoma cell / fibroblast) values. Each negative bar value corresponds to a significant enrichment of genes with the indicated annotation, with negative log₂(sarcoma cell / fibroblast) values, i.e., evidence for downregulation of genes with the indicated function in sarcoma-derived cultured cells vs. skin-derived fibroblasts