TCGA COAD

Eiram Noshein Elahi

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Oct 23, 2013, 5:26:45 AM10/23/13

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Hi,

I have downloaded ‘Colon Adenoma’ (COAD) data from TCGA portal using the data matrix.

I am now adding data from the cbioportal.org to identify samples with mutations (for e.g. BRAF). However, this holds data for both Colon and Rectum (not Colon only as TCGA). I am finding that the TCGA-sample ID’s don’t match between the two portals.

Could someone please let me know if there is a COAD equivalent dataset in cbioportal and how to access this?

Thank you and regards,

Eiram

Nikolaus Schultz

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Oct 23, 2013, 3:47:48 PM10/23/13

to cbiop...@googlegroups.com, Eiram Noshein Elahi

Dear Eiram,

The cBioPortal only has the combined COADREAD data set.

But you can always limit your analyses to subsets of the data, in your case the colon cancer samples.

Niki.

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Eiram Noshein Elahi

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Oct 24, 2013, 7:01:41 AM10/24/13

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Dear Nikolaus,

Thank you for the email and help.

The problem I have is that I have downloaded methylation files (450K) using TCGA (n=38, tumour and normal matched). Then by using cBioportal I want to selected cases with BRAF or KRAS mutations. However, none of the mutations match the cases in COAD data (by sampleID). I guess this is because the TCGA is COAD (Colon Adenoma) and cbioportal is COADREAD (Colon +Rectal adenoma).

I have tried to dissociate from the sample ID but no luck. I have built a case set by deselected cases concerning rectum (via query this study function), thereby only selecting colon cases from cbioportal, but still the IDs do not match. I have also entered Patient/Cases ID but these have all gone unrecognized.

Could you please provide me with a little more assistance on the sampleIDs and how to identify, for example colon cases (COAD) that have a BRAF and KRAS mutations from cBIoportal?