Question: TCGA Methylation Data CpG Islands
0
gravatar for engineer.khan
4.2 years ago by
Pakistan
engineer.khan40 wrote:

I have been using Methylation data from TCGA, but not getting any clue of matching a record to respective CpG Islands/gene. Can anyone guide there please?

gene • 3.1k views
ADD COMMENTlink modified 4.2 years ago by Charles Warden6.9k • written 4.2 years ago by engineer.khan40

which version of the methylation data have you downloaded? The level-3 data (well, certainly the lung version) contains mappings of the probe ids to gene symbols and to chromosomal positions

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by russhh4.5k

Yes level 3 of Breast/Ovary Cancer. Downloaded from ICGC

ADD REPLYlink written 4.2 years ago by engineer.khan40
2
gravatar for Charles Warden
4.2 years ago by
Charles Warden6.9k
Duarte, CA
Charles Warden6.9k wrote:

Last time I checked, TCGA uses 450k data for DNA methylation.  You can use the annotation file (.bpm) file to map the probes to CpG islands.

You can get the latest version from Illumina.  If you have a hard time tracking it down, I have an annotation file with the demo dataset in the COHCAP package:

http://sourceforge.net/projects/cohcap/

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Charles Warden6.9k

Thank you so much. I am going to check it and get back to you

ADD REPLYlink written 4.2 years ago by engineer.khan40
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