I was looking for expression levels for two genes involved in serous ovarian cancer data from TCGA via CBio portal. Based on a Z-score threshold of 2.0, I found the following percentage of samples (cases) have expression levels affected (UP or Down)
Case Set: Tumors with mRNA data (Agilent microarray): All samples with mRNA expression data (489 samples) CCNE1 - 11% CDK12 - 7%
For same dataset in Oncomine (I am using the free version):
TCGA Ovarian (517 samples <- this number is higher than what is reported in TCGA ovarian cancer publication) expression data is provided as log-2 median intensity and the in Oncomine shows that higher expression level of CCNE1 and CDK12 expression level is correlated with different grades - for example Grade 3 tumor (Grade 3 (431 samples) have higher expression level of both genes.
I have also noticed that the dataset 517 samples were assigned as No Associated Paper 2011/03/24. I am wondering if the data is reffering to this paper on TCGA ovarian cancer dataset. http://www.nature.com/nature/journal/v474/n7353/full/nature10166.html
I am wondering why such a discrepancy or am I missing something here.
PS. I have posted this question on both Oncomine and cBio list, but did not receive any responses yet. I am wondering if anyone here with experience on one of the platform could provide insight to this.