Oligonucleotide DNA microarray analyses

RNA was extracted from fresh frozen tumor tissue in the area of highest tumor purity. The bulk of samples had tumor content above 80%, and the minimum inclusion threshold was set to >50%. The RNA was hybridized to Agilent Whole Human Genome Microarrays according to instruction from the vendor (www.agilent.com). The arrays were then scanned by the Agilent Microarray Scanner Bundle. Intensity of the spot signal was interpreted by using the software J-Express (http://jexpress.bioinfo.no/site/).

Samples diagnosed by pathologist as CAH or EECG1 were selected, and unsupervised hierarchical clustering was conducted using Euclidean distance measurement. Transcriptional differences between two groups were explored by GSEA [17], applying pre-defined gene sets supplied by the MSigDB (www.broadinstitute.org/gsea/index.jsp). SAM was used to identify genes most differentially expressed in two groups of patients.