Coordination of DNA copy number and gene expression among subtypes.

<p>Each point represents one of the 26 subtype-associated copy number (CN) regions, which are colored by the subtype having the greatest absolute copy number (GACN). The vertical axis is the difference in median CN between the GACN subtype and other subtypes. For the genes in each region, the differences in median expression between the GACN subtype and other subtypes were calculated and the median of these differences is the value on the horizontal axis. The association of CN difference and gene expression difference across these regions was compared by a Spearman correlation test (two-sided <i>P</i>). Two example DNA regions are circled. Region 1q21–23 had GACN in Magnoid. Hepatoma-derived growth factor (<i>HDGF</i>) was one of the most Magnoid overexpressed genes in this region. CN and gene expression for <i>HDGF</i> is displayed in which each point is one tumor (B). Region 7p22-12 had GACN in Squamoid. Fascin (<i>FSCN1</i>) was the most Squamoid overexpressed gene in this region (C). For reference, black lines in (B, C) indicate median gene expression and DNA CN. LAD tumors with copy number and expression arrays from all cohorts were used (<i>n</i> = 362).