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Data from the DTP Molecular Target program.

Email questions concerning DTP's molecular targets program to: Molecular Target Team [moltarget@mail.nih.gov]

 

Primary molecular target data (excluding microarray data)

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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.ZIPA 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.

 

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:

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 U95A data from Novartis, averaged data (from triplicate arrays)

 

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:

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 #U214 (June 2008)

  

Microarray data - Affymetrix U95A data from Novartis, data from individual arrays

 

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:

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)