Fig. 1

EWSR1-NFATc2-positive sarcomas exhibit highly divergent transcriptomes from EWSR1-ETS-positive Ewing sarcomas. a t-SNE cluster analysis of Ewing sarcoma (EWSR1-ETS-positive) and other morphological mimics. All gene expression data were generated on Affymetrix HG-U133-Plus2.0 microarrays and simultaneously normalized using RMA and brainarray CDF [5], yielding one optimized probe-set per gene [13]. Gene expression data were filtered for a minimum tumor purity of 40% as determined by the ESTIMATE algorithm [14]. Principal component analysis (PCA) using all genes represented on this microarray platform was done and visualized with the Rtsne Bioconductor package in R¹⁵. DLBCL diffuse large B-cell lymphoma, ARMS alveolar rhabdomyosarcoma. b Comparison of gene expression levels of FOXG1, NR5A2, SOX5, VDR, and TFAP2 in EWSR1-ETS-positive Ewing sarcomas (EWS), EWSR1-NFATc2-positive sarcomas, and CIC-DUX4-positive sarcomas (GSE34620 and GSE60740). Data are presented as dot plots. Horizontal bars indicate median expression levels. Whiskers indicate the interquartile range