Question: is GDC portal have COLORECTAL (COADREAD) cancer ?
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gravatar for Chaimaa
15 days ago by
Chaimaa170
Chaimaa170 wrote:

Hello guys, Im very familiar with Broad institute portal, but now since i need to work with molecular profiles and clinical drug response data. now i learned how to obtain clinial drug response data from GDC portal https://portal.gdc.cancer.gov/ my cancer of interest is colorectal cancer (COADREAD) , but i found that this type of cancer is not availabe in this GDC portal ( primary site). i only find colon (coad) instead, is this right?

Another issue, if i want to get clinical drug response data from GDC portal and the molecular profiles of the same patient id from Broad insitutue firhose is this biologically reasonable and have no effect on the results or the quality control?

Appreciate any help!

cancer gene expression • 163 views
ADD COMMENTlink modified 6 days ago • written 15 days ago by Chaimaa170

please, Any help or any hints or a tutorial to read about this issue if that possible?

ADD REPLYlink written 14 days ago by Chaimaa170
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gravatar for Kevin Blighe
14 days ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

Hello Chaimaa - good to see you again. I think that the COAD + READ are the TCGA cohorts that comprise 'COADREAD', or am I incorrect?

Here is a configured search. You can then further filter by Primary Site.

Edit: Here is a configured search for RNA-seq HT-Seq count files for just rectal cancer (READ).

Kevin

ADD COMMENTlink modified 14 days ago • written 14 days ago by Kevin Blighe56k

Hi @kevin, so happy to see you too, and I'm very thankful for the valuable information you provide here it really gives me always insightful biological knowledge. Here is the configured search i adopt to get for example COADREAD drug response data. However, i got 2 separate txt files, one is for coad drug response data and the second one is for read drug response data, So i have to combine both files together right? for further analysis?

ADD REPLYlink modified 6 days ago • written 6 days ago by Chaimaa170

Descriptive picture

ADD REPLYlink modified 6 days ago • written 6 days ago by Chaimaa170
1

Hey Chaimaa, yes, you can just combine the 2 files, like, row-bind them (rbind()). You should be able to link these to your expression data (or whatever other data that you have) via the UUID and / or TCGA barcode.

So, just to be pedantic for others: the COAD (COlon ADenocarcinoma) and READ (REctum ADenocarcinoma) (COADREAD) TCGA datasets are ultimately labeled under the common term of 'Colo-Rectal' Cancer, which are often studied together in real life.

ADD REPLYlink modified 6 days ago • written 6 days ago by Kevin Blighe56k

Great Thanks! @Kevin, very grateful for your usual help!.

Yes i want to do the analysis from an integrative view (gene expression, DNA methylation and somatic copy number alteration (CNV)) if the sample size was reasonable.

However, i yet don't know how to deal with GDC portal tcga data and even how to use JSON manifest, that what i really wan to learn. Thus, may be i will take these clinical informations with the corresponding samples (bcr_patient_barcode ) i find, and link them with the same samples from multi omics data (gene expression, DNA methylation and somatic copy number alteration (CNV) from BROAD firehose here, is it ok ?

ADD REPLYlink modified 6 days ago • written 6 days ago by Chaimaa170
1

Yes, it is not easy - I apologise on behalf of the National Cancer Institute.

With your JSON manifest file, you can use the data transfer tool to download data: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

The CNV data is even more difficult... can you confirm the specific file that you want to obtain?

If you have any other specific questions, let me know. I am aware that it is difficult.

ADD REPLYlink written 6 days ago by Kevin Blighe56k
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