Question: TCGA clinical feature meaning of "pct_tumor_invasion" for TCGA-UCEC project (Uterine Corpus Endometrial Carcinoma)
0
gravatar for Fdota
14 months ago by
Fdota0
Fdota0 wrote:

Hello,

I have searched the Data Dictionary Viewer from https://docs.gdc.cancer.gov/Data_Dictionary/viewer/, but I didn't find the description of the feature "pct_tumor_invasion" showing up in the "clinical patient" data for project TCGA-UCEC, does anyone know what this feature means? Thanks!!!!

clinical tcga • 722 views
ADD COMMENTlink modified 14 months ago by Kevin Blighe33k • written 14 months ago by Fdota0

Update 24th September 2018:

Yet another updated answer, with further information: A: TCGA patient variable data dictionary

ADD REPLYlink written 11 weeks ago by Kevin Blighe33k
1
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

If you want to search for one of those terms used by the TCGA, you should go by the CDE code assigned to each term, which should be listed in the third row of the clinical data that you downloaded. For pct_tumor_invasion in the endometrial cancer dataset that I have, the CDE ID is CDE ID 3104403.

Here is where you can search for these: https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html (if you use the CDE ID, search under the Public ID Search tab).

Kevin

ADD COMMENTlink written 14 months ago by Kevin Blighe33k

Thanks Kevin, I found the description of the term. May I ask where can I find those CDE ID? I am using GDCprepare_clinic function from "TCGAbiolinks" package by Bioconductor to get those datasets. That pct_tumor_invasion feature is in the "patient" dataset, if you know what dataset the CDE ID is in, like "drugs", "follow_ups", "radiations" or "new_tumor_events"? Thank you!!!

ADD REPLYlink written 14 months ago by Fdota0

No problem! I have never used TCGAbiolinks as I normally download the data myself from the GDC Data Portal using manifest files. However, the TCGA being the TCGA, they have lots of data to manage and are constantly re-organising the data. The original files that I downloaded are now in the GDC Legacy Archive.

HERE I have configured a link for all legacy endometrial cancer clinical data in 'biotab' format as they call it. These legacy files have 3 names for each column, one being the CDE ID. You can configure for other cancers using the Cases and Files tabs (at left)

The updated GDC Data Portal no longer appears to supply these types of files and instead provides the data as XML or JSON files for each individual patient. I do know that there were inconsistency issues with using the legacy biotab files though. It is nevertheless handy just to have them in order to look up the CDE IDs.

For TCGAbiolinks, CDE IDs appear around four-fifths of the way down on this page: https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/clinical.html#get_legacy_clinical_data However, they don't explicitly mention CDE IDs.

Hope that this helps.

ADD REPLYlink modified 14 months ago • written 14 months ago by Kevin Blighe33k

Thanks a lot, they are very helpful!

ADD REPLYlink written 14 months ago by Fdota0
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