Question: Does TCGA have MLH1 gene methylation data?
0
gravatar for Feng Xie
4.0 years ago by
Feng Xie0
Feng Xie0 wrote:

I have download clinical data of CRC & UCEC samples from TCGA, and I want to know whether the samples' MLH1 gene promoter is hypermethylated or not. Does the clinical data contain MLH1 gene methylation data? How can I get this data?

gene • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.0 years ago by Feng Xie0

All TCGA data are available in GDC. TCGA legacy methylation data are in the GDC legacy portal. The particular data you want to check is the HM450 or HM27 beta values. New GDC reannotated methylation data on hg38 are coming soon from the main data portal.

ADD REPLYlink written 3.9 years ago by Zhenyu Zhang270
2
gravatar for Shicheng Guo
4.0 years ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Now, all the TCGA data were stored in the database of GDC, they provided the supportive email as the following:

support@nci-gdc.datacommons.io

Any questions could be sent to this email.

ADD COMMENTlink written 4.0 years ago by Shicheng Guo8.3k
2
gravatar for Jordan Anaya
4.0 years ago by
Jordan Anaya1.1k
US/Charlottesville
Jordan Anaya1.1k wrote:

Have you tried using MEXPRESS? http://mexpress.be/

ADD COMMENTlink written 4.0 years ago by Jordan Anaya1.1k
1
gravatar for zwdzwd
4.0 years ago by
zwdzwd120
zwdzwd120 wrote:

Yes, HM450 data from TCGA does covers well MLH1 promoter.

For example, using chr3:37032436-37035929 (GRCh37) narrows down to 44 probes.

cg02103401,cg24607398,cg10990993,cg04726821,cg11291081,cg05670953,cg18320188,cg04841293,cg05845319,cg21109167,cg03901257,cg02279071,cg14751544,cg16764580,cg01302270,cg17641046,cg07101782,cg03497419,cg27586588,cg16433211,cg10769891,cg19132762,cg23658326,cg11600697,cg21490561,cg00893636,cg03192963,cg06791151,cg07064226,cg06108510,cg24985459,cg12790037,cg25202636,cg17621259,cg14671526,cg05906740,cg27331401,cg25837710,cg12851504,cg06590608,cg11224603,cg19208331,cg14598950,cg13846866

The data is currently unavailable because of the GDC transition and should become available soon.

ADD COMMENTlink written 4.0 years ago by zwdzwd120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1073 users visited in the last hour