Fig. 2

a Analysis of the pervasiveness of genes that are highly specific to the transformed cells across all eight patients based on differential expression analysis (see “Methods”; all genes displayed have eightfold specificity for the transformed cells). The colorbar represents the product of the x- and y-axes. SOX2 is the most pervasively detected gene specific to transformed glioma cells in these eight HGG patients. b Drop-out curve for the total population of transformed cells showing the characteristic sigmoidal shape that indicates how, for the majority of genes, higher expression (counts per thousand or CPT) leads to detection in a higher fraction of cells. Because the detection frequency of SOX2 is close to that of similarly expressed genes, SOX2 is unlikely to be associated with a specific subpopulation of transformed cells and the frequency with which it is expressed among transformed cells is likely to be underestimated by our data. c IHC analysis confirming widespread protein expression of SOX2 in tissue slices from the six of the eight HGG patients in our cohort from which tissue was available for staining. We note that a considerable fraction of unstained nuclei in these specimens appear to be associated with blood vessels