Gene sets for evaluating predictions of genes associated with the EWSR1-WT1 fusion

We used several types of benchmark gene sets to comprehensively evaluate our prediction of the EWSR1-WT1 fusion. First, because literature co-citation data have been widely used to infer gene-gene and gene-disease functional associations, we compiled 74 genes cited in at least one paper related to EWSR1-WT1 and 201 genes cited in at least one paper related to DSRCT to evaluate our prediction. All PubMed identification numbers of articles related to EWSR1-WT1 or DSRCT were first downloaded, and then are cross-referenced with the gene citation information from Entrez Gene (ftp://ftp.ncbi.nih.gov/gene/), which is composed of genes and corresponding cited literature. These two benchmark gene sets would help evaluate whether top genes in our prediction include genes known to be associated with EWSR1-WT1 fusion and are associated with the DSRCT oncogenesis. Second, 268 genes whose promoter regions were peak binding sites of WT1 by Chip-seq in the JN-DSRCT1 cell¹⁶ was used to evaluate our predictions of plausible EWSR1-WT1 direct targets. Third, we also used a set of 328 cancer-related genes compiled from KEGG cancer pathways to evaluate the association between cancer pathways and the fusion. Fourth, to evaluate our predictions of therapeutic targets in the fusion-associated pathways, we collected 194 target genes of 52 compounds that have been tested in clinical trials or used for the treatment of DSRCT (Supplementary Data 8). These target genes were compiled manually from the literature^14,29 and two public drug databases: DrugBank, and DGIdb⁴¹.