Does TCGA have MLH1 gene methylation data?

Question

[Feng Xie]

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?

[Zhenyu Zhang]

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.

Answer 1

[Shicheng Guo]

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

[e-mail]

Any questions could be sent to this email.

Answer 2

[Jordan Anaya]

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

Answer 3

[zwdzwd]

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.