Question: Cbio Portal Vs. Oncomine: Difference In Samples And Expression Data
1
gravatar for Khader Shameer
4.5 years ago by
Manhattan, NY
Khader Shameer17k wrote:

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.

tcga cancer • 7.8k views
ADD COMMENTlink modified 15 months ago by sudurika90 • written 4.5 years ago by Khader Shameer17k

I am not sure whether you have looked into this page http://www.mycancergenome.org/

ADD REPLYlink written 4.5 years ago by vipin.ts40

And how would that page help, if they had?

ADD REPLYlink written 4.5 years ago by Neilfws47k
1
gravatar for Alex Ishkin
4.5 years ago by
Alex Ishkin10
San Diego
Alex Ishkin10 wrote:

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 :)

ADD COMMENTlink written 4.5 years ago by Alex Ishkin10

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.

ADD REPLYlink written 4.5 years ago by Khader Shameer17k
0
gravatar for sudurika9
15 months ago by
sudurika90
sudurika90 wrote:

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

ADD COMMENTlink written 15 months ago by sudurika90
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