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 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.
There can be several reasons for this discrepancy. I use neither Oncomine nor cBio, so I can't tell for sure, but I'd suggest that ovarian TCGA data set might be deposited to Oncomine from TCGA data portal, not from publication. The TCGA content seems to evolve; for example, number of Agilent gene expression profiles for ovarian cancer right now approaches 600 (as displayed in TCGA's DataMatrix). By the way, numbers of samples in DataMatrix tool and actual files in TCGA public folder for bulk downloads don't quite match, so I can't even say precisely how many samples are there.
One more thing: there are two microarray gene expression data sets in TCGA: Agilent and Affymetrix (not counting Illumina microarrays and RNA-Seq data,which are less abundant for ovarian cancer). From your description, I can't tell which of them is in the Oncomine.
The best idea would be to download the latest (=largest) data set from the TCGA web site directly and use gene expression profiles from it (moreover if you want to show how the genes behave across subtypes/correlate with clinical data). Though, it may not be worth an effort if you only need these data once in life :)
Thanks Alex, this is useful. I also got similar response from Oncomine help-desk.
I am looking differential gene expression for a few genes (n=12). Both databases provides normalized data not as such differential gene expression data, I am thinking about raw data analyses to get the data.
Hello Khader, I have recently just started Datamining. I have been able to use cBioPortal for TCGA, but am having trouble with Oncomine. Can you tell me if there is a clear protocol to submit query's to look at data sets. I am interested in looking at two proteins involved in prostate cancer progression and have not been able to figure out how to submit a query and retrieve information from Oncomine. Also, you mentioned that you were using the free version, can you specify? Thanks Sudurika
I am not sure whether you have looked into this page http://www.mycancergenome.org/
And how would that page help, if they had?