Unsupervised clustering reflects the combined effect of multiple confounding influences on the transcriptome, including presence of necrosis, inflammatory cells, inclusion of brain parenchyma, etc. In order to clarify the specific relationship of EGFR, PDGFRA and NF1 mutations to the transcriptome in GBM, we derived distinct expression signatures associated with mutation/aberration of these genes among the set of 147 tumors for which mutation/aberration was found in one and only one of the three. Here, PDGFRA is linked to glioblastoma.