I am examining the TCGA Methylation (Glioblastoma multiforme) dataset, to assess whether we can use it as a means for identification of potential biomarkers for clinical development. The issue I have is that we, ourselves, don't (at least yet) run our own chips here, nor have we done any Illumina assay chip designs.
Is there a readily-available public reference-list database that I've missed, which will allow me to bridge from the Illumina Human Methylation 27/450 CG# identifier codes back to standard NCBI Gene/RefSeq? I recall that, in the early days of TaqMan assay development, the exact targets of the SNP assays were all proprietary, and the marriage of those assays to Illumina sequence identifiers was sometimes challenging, if one needed to identify actual targets to assess biological plausibility/relevance...
Hi Larry,
You should be able to extract this information from the ADF file. Please see the following link:
https://tcga-data.nci.nih.gov/tcga/tcgaPlatformDesign.jsp
Please let me know if you are still not able to find the information you need.
Best wishes,
Peter
Hi Larry,
You should be able to extract this information from the ADF file. Please see the following link:
https://tcga-data.nci.nih.gov/tcga/tcgaPlatformDesign.jsp
Please let me know if you are still not able to find the information you need.
Best wishes,
Peter
I have this data in XLS format, so if you need it, drop me a line at [email protected]
If you're interested in a non-cancer dataset, we have Illumina gene expression array data and 450K methylation data linked in our paper on human pluripotent stem cells:
Article Recurrent Variations in DNA Methylation in Human Pluripotent...
Hi!!
how to get download methylation data from TCGA database .i couldn't find methylation and expression data .
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