Fig. 2
TBX2 is targeted by rare focal amplifications and marked by a SE. a 4C-seq analysis showing reciprocal interaction between the promotor site and SE upstream of TBX2 in the NB CLB-GA and SK-N-AS cell lines using three different viewpoints. b Copy number ratio of the TBX2 locus in a pan-cancer dataset (CCLE) with high copy number for TBX2 in NB (green arrow) as compared to cell lines from other tumor entities. Boxplots are drawn as a box, containing the 1st quartile up to the 3rd quartile of the data values. The median is represented as a line within the box. Whiskers represent the values of the outer two quartiles maximized at 1.5 times the size of the box. If 1 or more values outside of the whiskers are present, then this is indicated with a single mark dot next to the implicated whisker. Number of samples for every entity is depicted below the boxplot. c Genome-wide methylation profile evaluated by reduced representation bisulfite sequencing (RRBS) of the TBX2 locus in a pan-cancer dataset (CCLE). TBX2 is covered by a low methylation profile in NB (green arrow) as compared to cell lines from other entities. Boxplots are drawn as a box, containing the 1st quartile up to the 3rd quartile of the data values. The median is represented as a line within the box. Whiskers represent the values of the outer two quartiles maximized at 1.5 times the size of the box. If one or more values outside of the whiskers are present, then this is indicated with a single mark dot next to the implicated whisker. Number of samples for every entity is depicted below the boxplot. d Significantly increased TBX2 expression levels in cases with both high stage disease (stage 3 and 4) and increased TBX2 copy number due to 17q gain (ANOVA, n = 218, p = 6.004e−5, chr17 gain log2 ratio > 0.3). e Log2 copy number ratio of a region on 17q with a focal amplification encompassing the protein-coding genes PPM1D, BCAS3, TBX2, C17orf82, TBX4, and NACA2, in a primary NB tumor case (58,654 Mb—59,730 Mb—hg19—log2 ratio 2.78)
