How do we browse different data from the same sample from TCGA ?

Question

[Zakaria Benmounah]

Ni hao for everyone!,

I have a computer science background and I would like to analyse different data (CNA, mRNA and miRNA) from the same sample of different patients with a specific cancer.

I've tried to browse data from TCGA, using this guide but it doesn't provide enough information (and even not friendly at all).

I'm wondering what kind of download is the more appropriate to this matter (bulk or matrix or...), and how to do it?

Cheers!

[komal.rathi]

I don't know why you were even looking at that guide, which I am sure is not meant to be looked at when you want to download data. Shouldn't you be looking at the TCGA Data Portal instead? Data Matrix is a very good way to download any data available via TCGA for a specific cancer.

[Zakaria Benmounah]

Thanks for your reply. indeed I'm using TCGA Data Portal, but when clicking on Apply in the link, I get stuck what does row/column mean?

[komal.rathi]

Are you able to set the filters according to your requirement (type of cancer, type of data i.e. either CNV, Expression, Methylation etc)? If yes, once you hit apply, you get a table with rows that are sample names and columns that represents the type of data that you used for filtering (i.e. DNA methylation, Gene Expression, Copy Number Variation etc). I think it is pretty clear.

Here is an example. Click on the icon below. I have set my parameters to show Lung Adenocarcinoma DNA Methylation, Gene Expression and CNV data. Everything is right there.

[Zakaria Benmounah]

thanks a lot komal.rathi that's too helpful for me.

Answer 1

[emekdemir]

You also might want to look at the cbioportal.org

Answer 2

[Denise CS]

And don't forget COSMIC, with mutation data and associated information from the literature with the added value of including data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) portals.