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. Author manuscript; available in PMC: 2015 Feb 9.
Published in final edited form as: Nat Commun. 2014 Jun 2;5:3904. doi: 10.1038/ncomms4904

Figure 2. 3q27.2 gain targets BCL6 but does not alter its expression or target-gene repression.

Figure 2

a) GISTIC Q-values are shown for DNA copy number loss (blue) and gain (red) on chromosome 3. The peak of 3q27.2 gain included the BCL6 oncogene, but not the previously described target FOXP1. b) Significance of 3q27.2 gain was contributed to by broad gains of chromosome 3 or the 3q arm in 76 tumors, as well as focal gains of 3q27 in 52 tumors. These gains were mutually exclusive to BCL6 translocation in the 21 tumors for which matching DNA copy number and fluorescence in situ hybridization data were available. Grey bars represent data not available. c) Increased DNA copy number of BCL6 was not associated with increased transcript abundance compared to cases with no gain. Box plots represent the mean +/− the interquartile range with whiskers extending to the minimum and maximum value. d) Gene set enrichment analysis (GSEA) of BCL6 target genes showed no significant repression within cases possessing BCL6 DNA copy number gain (GSEA FDR = 0.509). e) For the 58 tumors with matching BCL6 translocation status and gene expression profiling data, BCL6 transcript abundance was not increased in tumors with BCL6 translocation compared to tumors without BCL6 translocation. Box plots represent the mean +/− the interquartile range with whiskers extending to the minimum and maximum value. f) Tumors with BCL6 translocation (Trans.-Pos.) showed no significant repression of BCL6 target genes by GSEA (GSEA FDR = 0.642) compared to tumors without BCL6 translocation (Trans.-Neg.).