876976.fig.002
Figure 2: Identification of regions of interest in GBM dataset by swatCGH. The panels show representative swatCGH data for chromosome 7, showing copy number gain using data segmented by DNAcopy. Panel (a) shows the chromosome overview plot, representing the median aCGH profiles (top), sample recurrence plot (middle), and high-level CNA plot (bottom). Dashed lines in the middle panel represent 80% AT. Panel (b) is regional probe classification view of a copy number gain CRI on chromosome 7 (42–56 Mb). In panel (b) samples are clustered by probe classifications (green = gain; red = loss; grey = normal; yellow = high-level gain; cyan = high-level loss). The red box indicates the MRI identified for the region, linked by the arrow from the same region of the middle plot in panel (a). Panel (c) illustrates a hyperlink from the MRI to the ENSEMBL genome browser, provided in swatCGH output.