Fig. 2

Myxoid liposarcoma scaffold protein composition and scaffold-induced gene expression. A Classification of proteins detected in myxoid liposarcoma (MLS) scaffolds (n = 4) using mass spectrometry analysis. Proteins were classified (n = 2172), according to the PANTHER protein classification. All proteins categorized as extracellular matrix protein (n = 41) are listed. B Significantly over- and underrepresented categories, comparing MLS scaffold proteins with all protein-coding genes (background) using PANTHER overrepresentation test with a false discovery rate < 0.05. The category order is based on fold enrichment with the highest overrepresentation in MLS scaffolds shown to the left. C Principal component analysis of transcriptional profiles based on RNA sequencing of MLS scaffold- and monolayer-cultured cells, respectively, for HT1080 wild-type (WT), HT1080 eGFP, HT1080 FUS::DDIT3-eGFP, MLS 2645-94 and MLS 1765-92, n = 3–5. D Venn diagram showing gene regulation overlaps between scaffold- and monolayer-cultured cells in respective cell line. E Functional enrichment analysis using the Hallmark and Chemical and genetic perturbations gene set collections for the 186 scaffold-regulated genes. Top 5 categories are shown based on q-value. Size of dots indicate gene count. F Interaction network of the 186 scaffold-regulated genes generated by Cytoscape based on protein interaction data retrieved from STRING. Node size is based on between-ness centrality, where a large node size indicates many interactions within the network. Purple nodes show proteins expressed in scaffolds. Common properties of adjacent proteins are indicated in blue, assessed from NCBI gene summary and UniProtKB/Swiss-Prot summary for each gene retrieved from GeneCards