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Fig. 1DWnt pathway and RUNX gene alterations in a pan-cancer analysis of the TCGA database. Top 20 cancer types where alterations in Wnt pathway components (A) or all three RUNX genes (B) are most frequently observed, including matched information on the percentage of samples with reciprocal RUNX/Wnt alterations. Shown in bold are the cancer types that appear in both top 20 lists. (C) The top 20 cancer types with RUNX alterations were each analysed for their percentage alteration of individual RUNX genes (RUNX1, blue; RUNX2, orange; RUNX3, green). Note that alterations of the RUNX genes are not always mutually exclusive and there can be cooccurrence in RUNX alterations (as demonstrated in ). Therefore, the maximum alteration frequency (%) displayed in Figure 1C is not necessarily representative of the total RUNX alteration frequency in Figures 1A and 1B, particularly in cancer types where more than one RUNX family member is altered. (D) A co-occurrence matrix was generated to observe co-occurrence between alterations in RUNX genes and listed Wnt pathway components in a pan-cancer analysis. The heat map, showing the log2 odds ratio, quantifies how strongly the presence or absence of alterations in gene X are associated with the presence or absence of alterations in gene Y. The heat maps are displayed only in the boxes of gene matches where the co-occurrence or mutual exclusivity was shown to be significant using the q-values (Derived from Benjamini–Hochberg false discovery rate [FDR] correction procedure). Wnt pathway components were selected for these analyses from the Wnt homepage, created by the Nusse Lab (http://web.stanford.edu/group/nusselab/cgi-bin/wnt/). All data for this figure was obtained through cBioPortal for Cancer Genomics (https://www.cbioportal.org/) using the TCGA PanCancer Atlas Studies (Cerami et al., 2012; Gao et al., 2013).
Mol. Cells 2020;43:188~197 https://doi.org/10.14348/molcells.2019.0310
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