A Gene Expression Database for the Molecular Pharmacology of Cancer

Nature Genetics, volume 24, no 3  March 1st, 2000 pp:236-244 (abstract)

 

Use of the Tools below requires registration.
Forgot your username or password?
This site is currently under construction, so please check back as improvements are made and capabilities are added.
We welcome comments and suggestions.

To download the compressed databases, right-click and choose 'save as' (PC) or hold down 'control' and click (Mac).

Link Description
Manuscript and Enlarged Figures
Text of manuscript with figures (PDF file)
Figure 1. The NCI Cancer Drug Discover - Development Pipeline (PDF)
     Legend
Figure 2. Cluster trees of cells on the basis of genes (A) and drugs (B) (PDF)
      Legend
Figure 3. Cluster trees of drugs on the basis of cells (A) and genes (B) (PDF)
      Legend
Figure 4. Color-coded clustered image map (CIM) relating 118 "mechanism of action" drugs to 1375 genes  (PDF)
      Legend
Figure 5. Scatter plot of L-Asparaginase (drug) and Asparagine Synthetase (gene) (PDF)
     Legend
  Table 1. Database for drugs analyzed in this study in Excel format
    
Databases
* If you downloaded *.sit or *.sit.bin file, double click the file icon to generate text file.
  Drug activity data (A-matrix), tab delimited (1400 drugs x 60 cells)    (687 Kb)
  Description                Click on icon to view    *** UPDATED 12/19/01 ***   (Download compressed:   PC/UNIX   Mac)   (previous version)               
  Drug activity data of 118 "Mechanism of Action" drugs, tab delimited (118 drugs x 60 cells )  (33 Kb)
  Description                Click on icon  to view    *** UPDATED 12/19/01 ***   (Download compressed:   PC/UNIX   Mac)   (previous version)              
  Gene expression data (T-matrix), tab delimited (1375 genes x 60 cells)    (579 Kb)
  Description                Click on icon to view  *** UPDATED 12/19/01 ***      (Download compressed:   PC/UNIX)   (previous version)               
  Target matrix (15 Kb)
  Description                Click on icon to view  *** UPDATED 01/09/02 ***      (Download compressed:   PC/UNIX)               
  Gene expression data (all genes, 9,706), tab delimited  (9,706 genes x 60 cells )   (6.4 MB)
  Description               Click on icon to view    *** UPDATED 12/19/01 ***   (Download compressed:   PC/UNIX   Mac)   (previous version)               
  Gene-drug correlation data (AT-matrix), tab delimited (1375 genes x 118 drugs)   (1.1 Mb)
  Description                Click on icon to view   (Download compressed:   PC/UNIX   Mac)              
Tools For Data Analysis And Visualization
  Generate a color-coded "Clustered Image Map" to explore patterns of gene-gene, drug-drug, or gene-drug relationship in the NCI60 data sets.
  For your favorite drug or gene: search for high positive and negative gene-gene, drug-drug, or gene-drug correlations.
  Display correlation statistics and scattergram for a drug/gene/cell pair (i.e., a drug-drug, gene-gene, cell-cell, drug-cell, or gene-cell pair)
  Upload your own data set and generate a Color-Coded Clustered Image Map (CIM) for single matrix
  Upload your own data sets and generate a Color-Coded Clusterd Image Map (CIM) for multiple matrix (Under construction)
  Upload your own data set and generate a Color-Coded Image Map (CIM) for no cluster
Links
  Nature Genetics
  Stanford Genomic Resources
  The NCI Developmental Therapeutics Program
  Gene Chips microarray review site
  DCS/CIT microarray databases and tools