I Want To Get Mirna- Mrna Expression From One Sample In One Experiment From Tcga, But It'S Seems That, The Experiment Centers Are Diffrent.Any Help?

Question

[jack]

Hi all,

I want to get the miRNA-mRNA expression which measured in one sample from TCGA,(paired sample ), but when I looked at them the experiment center are diffrent. for example for mRNA is UNC and for miRNA is BCGSC.

what I exactly want is like this :

for example for breast cancer :

Sample       miRNA(UNC)        mRNA(UNC)

A                 A                A  
B                 A                A
C                 A                A
D                 A                A
.
.

But what TCGA showes me is like :

Sample       miRNA(BCGSC)        mRNA (UNC)

A                 A                A  
B                 A                A
C                 A                A
D                 A                A

[Michael]

What do you mean by "experiment center"? The sequencing lab? Why is that relevant, or surprising, is there anything that could be done at all? If at all relevant, which dataset is it exactly?

[jack]

what I understood is that : UNC/ BCGSC is the centre where they measured gene expression. and what I need is the expression of miRNA-mRNA measured in one sample. with one sample, I mean in one experiment they extracted miRNA and mRNA and sequenced it, not like that they got miRNA expression form one sample and mRNA expression from other sample of the same cancer. since the sequencing centre are different, I doubt that how could it possible that miRNA-mRNA measurement come from same(one) sample.but interesting thing is that, the sample ID is the same, which in principle would mean that for every sample, they measured miRNA-mRNA expression.

[Michael]

So you are trying to avoid batch effects?

Answer 1

[Charles Warden]

TCGA splits up the work for each technology to a different center for data production and analysis (in almost all cases). The examples you have shown above do in fact come from the same patient, but they were processed at different centers throughout the country for the different parts of the analysis.

For example, here are the different centers were some of the data types are processed:

http://cancergenome.nih.gov/abouttcga/overview/howitworks/characterizationcenters

For example, DNA methylation data is never processed at either of the centers described you mentioned - it is produced at USC (and some might have been produced at Johns Hopkins, but they currently only list USC - but the point is that the same samples are processed at different centers)

This page provides an overview, with links such as the one provided above:

http://cancergenome.nih.gov/abouttcga/overview

That said, every patient won't have paired data for every technology. For example, you can see the sample counts vary for each technology for breast cancer (although the sample counts now seem more similar than I have remembered in the past):

https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=BRCA&diseaseName=Breast%20invasive%20carcinoma