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Figure 8 | Genome Medicine

Figure 8

From: Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

Figure 8

Copy number changes in GNS cell lines correlate with gene expression levels. (a) Curves show distributions of expression level differences between GNS and NS cells, stratified by aberration calls. The distributions for genes in segments without aberrations (neutral) peak near the 0 mark, corresponding to an equal expression level in GNS and NS cells. Conversely, genes in lost and gained regions tend to be expressed at lower and higher levels, respectively. In each plot, log2 fold changes were computed between the indicated GNS cell line and the mean of the two NS cell lines, and capped at (-8, 8) for visualization purposes. To obtain robust fold-change distributions, genes with low expression (<25 tags per million) in both cancer and normal cell types were excluded; consequently, between 6,014 and 6,133 genes underlie each plot. (b) For each of the three gene sets listed in the legend (inset), bars represent the percentage of genes with the indicated copy number status. (c) Aberration calls for the 29 genes broadly distinguishing GNS from NS cells by qRT-PCR. Circles indicate focal (<10 Mb) aberrations; boxes indicate larger chromosomal segments.

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