Deletion properties that distinguish common fragile site genes from tumor suppressor genes.

<p>Scatter dot plots of values for statistics that distinguish focal deletions affecting common fragile site (CFS) genes (orange) from tumor suppressor genes (blue). (A) “RNA/DNA Correlation,” which corresponds to the Pearson’s correlation coefficient of log2-transformed DNA copy number values and relative RNA expression values for the 115 tumor samples with both array CGH and RNA expression profiling data, (B) DNA Copy Number is the median value of segmented DNA copy number values. (C) Cell Line Proportion” which provides a relative measure of how frequently deletions for a given gene are found in cell lines rather than primary tumors. Panels (D) and (E) show the number of deletions found in each gene within a 10 Mb region centered on the <i>MACROD2</i> locus (D) and TP53 and <i>MAP2K4</i> loci (E). (F) Box and whisker plots of “Deletion Isolation,” which measures how frequently neighboring genes are deleted relative to the featured gene.