Fig A4.

Full candidate pathway that represents molecular drivers of tumorigenesis in the sarcoma of patient 1. We reconstructed this pathway on the basis of the outlier analysis, differential gene expression analysis, copy number information and literature mining (Appendix Methods).A simplified version of this pathway is presented in Figure 3A. Both EWSR1-ATF1 and receptor tyrosine kinases PDGFRB, NTRK1, ALK, and FGFR1 can contribute to the activation of IL6/JAK/STAT3 signaling. All gene expression outliers depicted in this figure were significant in all three comparisons: patient 1 versus all cancers, patient 1 versus lung adenocarcinomas, and patient 1 versus sarcomas. JAK1, the molecular target of ruxolitinib, is indicated with a yellow lightning bolt. TCGA, The Cancer Genome Atlas.