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Gene expression data (array based) refers to transcriptional level expression, i.e., the abundance of transcripts. Gene expression can be measuredĀ at transcription level (mainly mRNA) and translation level (protein).

Data Overview

Currently, there are multiple microarray platforms designed to measure gene expressions at mRNA level. In TCGA projects, both single channel and two-channel microarray platforms are used. In a typical two channel microarray platform,  the two samples (one from the target sample and the other from reference sample) are labeled with Cy3 and Cy5 and mixed, and then hybridized to a single microarray. The relative intensities of Cy3 and Cy5 are then used in ratio-based analysis to identify up-regulated and down-regulated genes. In single-channel microarrays, only one sample is labeled and hybridized to a microarray. The fluorescent intensity of a given gene does not indicate the abundance of the gene in the sample, but rather its relative abundance when compared to other samples. Therefore, its data normalization method is very different from a two-channel platform. Affymetrix HG-U133-Plus2 is an example of a single channel platform.

Available Platforms

Platform Code

Platform Alias

Platform Name

Available

Example

FTP Display

HT_HG-U133A

HT_HG-U133A

Affymetrix HT Human Genome U133 Array Plate Set

YES

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
ht_hg-u133a/transcriptome

HG-U133_Plus_2

HG-U133_Plus_2

Affymetrix Human Genome U133 Plus 2.0 Array

YES

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-u133_plus_2/transcriptome/

AgilentG4502A_07_1

AgilentG4502A_07

Agilent 244K Custom Gene Expression G4502A-07-1

YES

example icon


/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_1/transcriptome

AgilentG4502A_07_2

AgilentG4502A_07

Agilent 244K Custom Gene Expression G4502A-07-2

YES

[!example.png|alt="example icon"! (http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<disease_study>/cgcc/unc.edu/agilentg4502a_07_2/transcriptome/)]


/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_2/transcriptome

AgilentG4502A_07_3

AgilentG4502A_07

Agilent 244K Custom Gene Expression G4502A-07-3

YES

example icon


/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_3/transcriptome

HuEx-1_0-st-v2

HuEx-1_0-st-v2

Affymetrix Human Exon 1.0 ST Array

YES

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
huex-1_0-st-v2/exon

Examples of Array Based Expression Data Files

Leve 1 Data

Platform

File Extension

Example

FTP Display

HT_HG-U133A

.CEL

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
ht_hg-u133a/transcriptome

HG-U133_Plus_2

.CEL

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-u133_plus_2/transcriptome

AgilentG4502A_07_1

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_1/transcriptome

AgilentG4502A_07_2

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_2/transcriptome

AgilentG4502A_07_3

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_3/transcriptome

HuEx-1_0-st-v2

.CEL

Controlled access example icon

/tcgafiles/ftp_auth/
distro_ftpusers/tcga4yeo/tumor/
<disease_study>/cgcc/<domain>/
huex-1_0-st-v2/exon


Level 2 Data

Platform

File Extension

Example

FTP Display

HT_HG-U133A

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
ht_hg-u133a/transcriptome

HG-U133_Plus_2

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
hg-u133_plus_2/transcriptome

AgilentG4502A_07_1

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_1/transcriptome

AgilentG4502A_07_2

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/
tumor/<disease_study>/cgcc/<domain>/
agilentg4502a_07_2/transcriptome

AgilentG4502A_07_3

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_3/transcriptome

HuEx-1_0-st-v2

.txt

Controlled access example icon

/tcgafiles/ftp_auth/
distro_ftpusers/tcga4yeo/tumor/
<disease_study>/cgcc/<domain>/
huex-1_0-st-v2/exon

LeveL 3 Data

Platform

File Extension

Example

FTP Display

HT_HG-U133A

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
ht_hg-u133a/transcriptome

HG-U133_Plus_2

.txt

Not available

Not available

AgilentG4502A_07_1

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_1/transcriptome

AgilentG4502A_07_2

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_2/transcriptome

AgilentG4502A_07_3

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
agilentg4502a_07_3/transcriptome

HuEx-1_0-st-v2

.txt

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
huex-1_0-st-v2/exon

Specific Validations

Array based gene expression data follows standard validation processes described below. It has no data type-specific validations.

Standard Validations

Array based expression data archives undergo standard validation processes described in the Standard Archive Validation.

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