Question: How do we browse different data from the same sample from TCGA ?
0
gravatar for Zakaria Benmounah
4.6 years ago by
United Kingdom
Zakaria Benmounah50 wrote:

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!  

 

browse data tcga • 1.4k views
ADD COMMENTlink modified 4.6 years ago by Denise - Open Targets5.0k • written 4.6 years ago by Zakaria Benmounah50
1

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.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by komal.rathi3.4k
1
gravatar for emekdemir
4.6 years ago by
emekdemir100
United States
emekdemir100 wrote:

You also might want to look at the cbioportal.org

ADD COMMENTlink written 4.6 years ago by emekdemir100
1
gravatar for Denise - Open Targets
4.6 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

And dont 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. 

ADD COMMENTlink written 4.6 years ago by Denise - Open Targets5.0k
0
gravatar for Zakaria Benmounah
4.6 years ago by
United Kingdom
Zakaria Benmounah50 wrote:

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? 

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Zakaria Benmounah50
1

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.

 

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by komal.rathi3.4k
0
gravatar for Zakaria Benmounah
4.6 years ago by
United Kingdom
Zakaria Benmounah50 wrote:

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

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Zakaria Benmounah50
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