Fig. 1

Principal components analysis (PCA) and gene functional annotation enrichment analysis of the transcriptomes of FISS and normal tissue. a Bars indicate the percentage of the variance of gene expression level data across the six tissue samples that is explained by each of the six principal components (PCs). Over 70% of the variance is explained by the combination of principal components 1 and 2 (PC1 and PC2). b PCA loading scores for each of the samples, for PC1 and PC2. Each mark corresponds to a sample, with mark shape indicating sample tissue type (see legend). Ellipses indicate groupings of normal tissue and sarcoma tumor samples. The normal skin tissue ellipse is highly eccentric due to separation between muscle and skin tissues. The sarcoma sample group ellipse is not visible due to the tight clustering of sarcoma samples in the loading plot. c Significant positive functional annotation enrichment scores based on Gene Set Enrichment Analysis (GSEA) of gene-level differential expression log₂(sarcoma/skin) values, using ortholog mapping and human gene functional annotations from the Gene Ontology. Bar magnitude indicates the annotation’s normalized enrichment score from GSEA; 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/skin) values, i.e., evidence for upregulation of genes with the indicated function in sarcoma vs. normal tissue. d Significant negative functional annotation enrichment scores based on GSEA of gene-level log₂(sarcoma/skin) values. Each negative bar value corresponds to a significant enrichment of genes with the indicated annotation, with negative log₂(sarcoma/skin) values, i.e., evidence for downregulation of genes with the indicated function in sarcoma vs. normal tissue