Extended Data Fig. 8: Examples of neo-loop-involved genes.
a, (left) Reconstructed Hi-C map for the translocation (chr19: 6.62M, -; chr11: 118.91M, -) in a T-ALL (T-cell Acute Lymphoblastic Leukemia) patient. Blue circles indicate the predicted neo-loops. (middle) Kaplan-Meier survival analysis of TCGA leukemia patients with high (top 35%) and low (bottom 35%) expressions of the UPK2 gene. The means and the 95% confidential intervals are shown for each group of patients. The p-value was calculated from two-sided log-rank test. (right) Log2 converted copy number ratios of the UPK2 gene with high (top 35%) or low (bottom 35%) expressions in patients. The horizontal bar in each violin plot represents the median. Genes with higher expression levels do not have higher copies. The p-value was computed from two-sided Mann-Whitney U test. b-c, Similar examples in a gastric cancer patient T2000877. The Kaplan-Meier survival and copy-number analysis were performed using TCGA stomach adenocarcinoma patient data.
