Fig. 3

The pattern of differential expression in FISS tumors vs. normal skin tissue is consistent with the pattern of differential expression in FISS-derived cells vs. fibroblast-derived cells. a Each mark represents one of 335 genes that are all differentially expressed (FDR < 0.05) between the sarcoma and normal sample groups, in tissues (i.e., the comparison of sarcoma tumors vs. skin samples) and in cultured cells (i.e., the comparison of FISS-derived cell lines vs. skin-derived fibroblasts). Each data mark’s position on the horizontal axis corresponds to the log₂(sarcoma/skin) value for the gene in tissue, and on the vertical axis corresponds to the log₂(sarcoma cell / fibroblast) value for the gene in cultured cells. Overall counts of the number of genes within each quadrant are shown. b Heatmap visualization including individual gene names, with cell colors indicating the log₂(individual sample / average across all samples) for each of 335 genes (columns) across 14 samples (rows). Red indicates upregulation vs. the sample average, and blue indicates downregulation vs. the sample average (no change from sample average is mapped to white). Genes are ordered by sign of primary tissue log₂(sarcoma/skin) ratio, then by sign of log₂(sarcoma cell / fibroblast) ratio in cultured cell samples, and then overall average log₂(sarcoma/normal) ratio. Abbreviations: “fiss_line”, FISS-derived cell line; “fibrobls.”, fibroblast cells; “sarcoma”: FISS tumor tissue; “skin”: normal skin tissue