question about validation of differentially expressed genes

Question

[tujuchuanli]

Hi,

I did differentially expression (DE) analysis on TCGA datasets and identified several DE genes. During my paper review, one of reviewers insisted on the validation of DE genes by experiment.

To be honest, I do not have place, equipment and so on to do this validation. So I have a Plan-B which is validated at least some of DE genes which really exist in other datasets or databases.

How do you think of this idear?

Do you have some existed databases or tools to query or download the DE genes in other datasets especially for cancer types in TCGA?

Thanks in advance

[Kevin Blighe]

You don't have funds to develop some primers and probe to run a real-time PCR for a simple validation, or even collaborate internally? Validation in already-existing datasets is an additional level that is quite standard these days. To quicken the pace, you could take a look at the data in cBioPortal.

[ATpoint]

Please provide some details. What does your paper deal with? What kinds of cancers did you analyze? In general, you of course cannot verify TCGA results because you have no access to the original RNA. Did you clearly state in the manuscript that the data are from TCGA and not produced by yourself? Given you strictly have no option with a collaborator to do vadilation exeriments, maybe in a couple of related cell lines, I would try to find data from other publications or consortia to at least reproduce the general patterns you found.