DTP - Download Page for Molecular Target Data

Download Page for Molecular Target Data

August 2010 Data Release (Release Notes)

Overview of the Datasets

Data from Large Scale Experiments

mRNA expression measured on microarrays
- Affymetrix U133 - measured by Chiron
- Affymetrix U133 - measured by GeneLogic
- Affymetrix U95A-E - measured by GeneLogic
- Affymetrix U95A - measured by Novartis.
  - Data was performed in triplicate. Both averaged and individual datasets are provided.
- cDNA array - measured by Weinstein, Brown and Botstein labs
- Affymetrix HUM6000 - measured by Millenium
SNP array of 120k features - measured by Sellers lab
- Allele calls
- Estimated DNA copy number
- Identifiers
Array CGH DNA copy number- measured by Gray and Weinstein labs
Estimated DNA copy number extracted from karyotypes - karyotypes determined by Kirsch lab.

Data from Smaller Scale Experiments

All small-scale measurements (includes protein, mRNA, miRNA, DNA methylation, mutations, SNPs, enzyme activity, metabolites).
Subsets containing just:
- Protein data
- DNA data
- DNA methylation data -measured by Sequenom
- miRNA data - measured by Israel lab and by Weinstein and Croce labs
- Metabolite data - measured by Metabolon
  - Data was perfomred in triplicate. Both averaged and individual datasets are provided.

Overview of the Datasets

Primary molecular target data (excluding microarray data) includes protein, mRNA, miRNA, DNA methylation, mutations, SNPs, enzyme activity, metabolites

WEB_DATA_ALL_MT.ZIP

A 3.4 Mb zip file -
The uncompressed file is approximately 82.7 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), GENE, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, GeneID, UNITS, METHOD, VALUE, TEXT

Protein Data Only A subset of WEB_DATA_ALL_MT containing just the protein data

WEB_DATA_PROTEIN.ZIP -

A 219 Kb zip file -
The uncompressed file is approximately 3.2 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), GENE, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, GeneID, UNITS, METHOD, VALUE, TEXT

DNA Data Only A subset of WEB_DATA_ALL_MT containing just the DNA data

WEB_DATA_DNA.ZIP

A 26 kb zip file -
The uncompressed file is approximately 580 Kb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), GENE, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, GeneID, UNITS, METHOD, VALUE, TEXT

DNA Methylation Data From Sequenom A subset of WEB_DATA_ALL_MT containing just the DNA methylation data, Proc Natl Acad Sci USA 2008, Mar 25; 105(12): 4844-9.

WEB_DATA_SEQUENOM_METHYLATION.ZIP

A 5.2 Mb zip file -
The uncompressed file is approximately 43.8 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), GENE, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, GeneID, VALUE

microRNA Data From the Israel Lab A subset of WEB_DATA_ALL_MT containing just the microRNA data from the Israel lab. Cancer Res. 2007, Mar 15; 67(6): 2456-68.

WEB_DATA_ISRAEL_MIR.ZIP

A 98 Kb zip file -
The uncompressed file is approximately 1.1 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, UNITS, METHOD, VALUE, TEXT

microRNA Data From the Weinstein and Croce Labs A subset of WEB_DATA_ALL_MT containing just the microRNA data from the Weinstein and Croce labs. Mol Cancer Ther 2007, May; 6(5): 1483-91.

WEB_DATA_CROCE-WEINSTEIN_MIR.ZIP

A 601 Kb zip file -
The uncompressed file is approximately 6.3 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, ENTITY_MEASURED, UNITS, METHOD, VALUE, TEXT

Metabolomic Data From Metabolon- data averaged from triplicate experiments A subset of WEB_DATA_ALL_MT containing just the metabolomic data from Metabolon.

WEB_DATA_METABOLON.ZIP -

A 171 Kb zip file -
The uncompressed file is approximately 1.2 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, VALUE, STD DEV

Metabolomic Data From Metabolon - individual data from each of the triplicate experiments

WEB_DATA_METABOLON_ALL.ZIP

A 404 Kb zip file -
The uncompressed file is approximately 3.2 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: SAMPLENAME, TITLE, PANELNBR, CELLNBR, pname, cellname, VALUE

THE FOLLOWING DATASETS ARE DERIVED FROM LARGE-SCALE EXPERIMENTS

Estimated chromosomal band copy number, extracted from spectral karyotyping
Cancer Res 63, 8634-47 (2003).

Data is provided as an Excel file listing copy number of each chromosomal band for each cell line. Download excel file

Affymetrix 125K SNP array data from the Sellers' lab
Nature 436, 117-122 (2005).

Data is provided as 3 datasets: Copy number, allele calls and identifiers.

The Copy Number Data:

COPYNUM.ZIP

A 51.6 Mb zip file -
The uncompressed file is approximately 307 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MARKER, CellID, COPYNBR, PANELNBR, CELLNBR, pname, cellname

The Allele Call Data:

ALLELECALL.ZIP

A 29.6 Mb zip file -
The uncompressed file is approximately 290 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MARKER, CellID, AlleleCall, PANELNBR, CELLNBR, pname, cellname

The Identifiers Data:

IDENTIFIERS.ZIP

A 3.6 Mb zip file -
The uncompressed file is approximately 11 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MARKER, RefSNPID, Chromosome, Chromosome Location, Allele_A, Allele_B, FlankingSeqA, FlankingSeqB

Array CGH DNA copy number data
(relative to normal female DNA) from the Weinstein (NCI) and Gray (UCSF) labs
Mol Cancer Ther. 2006 Apr;5(4):853-67.)

CGH_COPYNUM.ZIP

A 105 Kb zip file -
The uncompressed file is approximately 1.0 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), GENE, CHROMOSOMAL LOCATION, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, cellname, pname, VALUE

Microarray Data- Affymetrix U133 array data from Chiron Data was processed with the Affymetrix MAS5 algorith, with a scaling factor of 100.

WEB_DATA_CHIRON.ZIP

A 21.9 Mb zip file -
The uncompressed file is approximately 305 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), ACC, GENE, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, CHIP, FEATURE_ID, UniGene, GeneID, PRESENT_CALL, VALUE
Gene assignments are based on Unigene Build #U225 (August 2010)

Microarray data- Affymetrix U133 array data from Gene Logic, Inc. Data was processed with the Affymetrix MAS5 algorith, with a scaling factor of 100.

WEB_DATA_GENELOGIC_U133.ZIP

A 26.0 Mb zip file -
The uncompressed file is approximately 314 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), ACC, Gene, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, CHIP, FEATURE_ID, UniGene, GeneID, VALUE
Gene assignments are based on Unigene Build #U225 (August 2010)

Microarray data - Affymetrix U95 array data from Gene Logic, Inc. Data was processed with the Affymetrix MAS5 algorith, with a scaling factor of 100.

WEB_DATA_GENELOGIC_U95.ZIP

A 34.1 Mb zip file -
The uncompressed file is approximately 401 Mb.

When uncompressed the file is comma delimited in the following format:

Microarray data - Affymetrix U95A data from Novartis, averaged data (from triplicate arrays) Data was processed with the Affymetrix MAS5 algorith, with a scaling factor of 100.

WEB_DATA_NOVARTIS.ZIP

A 9.4 Mb zip file -
The uncompressed file is approximately 84 Mb.

When uncompressed the file is comma delimited in the following format:

Microarray data - Affymetrix U95A data from Novartis, data from individual arrays (from which the averaged data, above, was generated).
Data was processed with the Affymetrix MAS5 algorith, with a scaling factor of 100.

WEB_DATA_NOVARTIS_ALL.ZIP -

A 26.8 Mb zip file -
The uncompressed file is approximately 145 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: Probe Set Name, ID (composite of the moltid derived from this measurement, and a letter to distinguish individual arrays), GENE, cellname, pname, PANELNBR, CELLNBR, Signal, Detection, P value
Gene assignments are based on Unigene Build #U225 (August 2010)

Microarray data - cDNA array data from the Weinstein (NCI) and Brown & Botstein (Stanford) groups
Nat Genet. 2000 Mar;24(3):236-44.
Nat Genet. 2000 Mar;24(3):227-35.
Units are log2 of singal from the test cell/reference pool

WEB_DATA_STANFORD.ZIP

A 5.5 Mb zip file -
The uncompressed file is approximately 60.1 Mb.

When uncompressed the file is comma delimited in the following format:

File Format: MOLTID (NCI pattern #), ACC, Gene, TITLE, MOLTNBR(NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, CHIP, FEATURE_ID, UniGene, GeneID, VALUE
Gene assignments are based on Unigene Build #U225 (August 2010)

Microarray data - Affymetrix HUM6000 array data from Millenium Pharmaceuticals

Details of this experiment.

WEB_DATA_MILLENIUM.ZIP

A 4.2 Mb zip file -
The uncompressed file is approximately 47.2 Mb.

When uncompressed the file is comma delimited in the following format:

Email questions concerning DTP's molecular targets program to: Susan Holbeck [holbecks@mail.nih.gov]

Molecular Targets

Overview of the Datasets

Data from Large Scale Experiments

Data from Smaller Scale Experiments

Overview of the Datasets

THE FOLLOWING DATASETS ARE DERIVED FROM LARGE-SCALE EXPERIMENTS