FLI1 and Ewing sarcoma: By examining the gene correlations along PHATE_1 in Ewing sarcoma cells (Table S2), we discovered several genes strongly correlated with an EWSR1-FLI1-high cell state which are relevant to R-loop resolution and replication stress: 1) the Fanconi Anemia pathway (FANCI, FANCD2, and FANCA), and 2) Flap endonuclease 1 (FEN1).