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DNA methylation is an epigenetic mark which can be associated with transcriptional inactivity when located in promoter regions. In the context of TCGA, DNA methylation refers to the covalent modification of cytosine bases at the C-5 position, generally within a CpG sequence context.

Data Overview

DNA methylation data files contain information on raw and normalized signal intensities, detection confidence and calculated beta values for methylated and unmethylated probes. Level 3 data include masking of data, including SNP-related data. Details on data masking can be found in the DESCRIPTION.txt files that accompany data level and MAGE-TAB archives.

Besides generic validations for GCC archives, the DNA Methylation data type does not have any data type-specific checks.

Available Platforms

 

Platform Code

Platform Alias

Platform Name

Available

FTP Display

IlluminaDNAMethylation_OMA002_CPI

IlluminaDNAMethylation

Illumina DNA Methylation OMA002 Cancer Panel I

Yes

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
illuminadnamethylation_oma002_cpi/methylation/

IlluminaDNAMethylation_OMA003_CPI

IlluminaDNAMethylation

Illumina DNA Methylation OMA003 Cancer Panel I

Yes

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
illuminadnamethylation_oma003_cpi/methylation/

HumanMethylation27

HumanMethylation27

Illumina Infinium Human DNA Methylation 27

Yes

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
humanmethylation27/methylation/

HumanMethylation450

HumanMethylation450

Illumina Infinium Human DNA Methylation 450

Yes

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
humanmethylation450/methylation/

 

Data File Descriptions

 

Platform Code

Data Level

File Type

Description

Example

IlluminaDNAMethylation_OMA002_CPI

1

Tab-delimited, ASCII text (.txt)

Cy3 and Cy5 signals and detection confidence of methylated probes

example icon

IlluminaDNAMethylation_OMA002_CPI

2

Tab-delimited, ASCII text (.txt)

Calculated beta values

example icon

IlluminaDNAMethylation_OMA003_CPI

1

Tab-delimited, ASCII text (.txt)

Cy3 and Cy5 signals and detection confidence of methylated probes

example icon

IlluminaDNAMethylation_OMA003_CPI

2

Tab-delimited, ASCII text (.txt)

Calculated beta values

example icon

HumanMethylation27

1

Binary (.idat)

Intensity data file with statistics for each bead type in terms of bead count, mean and standard deviation per dye

example icon

HumanMethylation27

2

Tab-delimited, ASCII text (.txt)

Calculated beta values and mean signal intensities for replicate methylated and unmethylated probes

example icon

HumanMethylation27

3

Tab-delimited, ASCII text (.txt)

Calculated beta values, gene symbols, chromosomes and genomic coordinates (build 36). Some data have been masked (including known SNPs)

example icon

HumanMethylation450

1

Binary (.idat)

Intensity data file with statistics for each bead type in terms of bead count, mean and standard deviation per dye

example icon

HumanMethylation450

2

Tab-delimited, ASCII text (.txt)

Background-corrected methylated (M) and unmethylated (U) summary intensities as extracted by the methylumi package

example icon

HumanMethylation450

3

Tab-delimited, ASCII text (.txt)

Calculated beta values, gene symbols, chromosomes and genomic coordinates (hg18). Some data have been masked (including known SNPs)

example icon

Data Validation

 

Data Type-Specific Validations

Apart from the standard GCC validation set listed below, DNA methylation has no data type-specific validations.

Standard Validations

DNA Methylation archives undergo standard validation sets shown in the Standard Archive Validation chart for GCC archives:

 

 

 

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