multidrug: Multidrug Resistence Data

In mixOmicsTeam/mixOmics: Omics Data Integration Project

Multidrug Resistence Data

Description

This data set contains the expression of 48 known human ABC transporters with patterns of drug activity in 60 diverse cancer cell lines (the NCI-60) used by the National Cancer Institute to screen for anticancer activity.

Usage

data(multidrug)

Format

A list containing the following components:

list("ABC.trans")

data matrix with 60 rows and 48 columns. The expression of the 48 human ABC transporters.

list("compound")

data matrix with 60 rows and 1429 columns. The activity of 1429 drugs for the 60 cell lines.

list("comp.name")

character vector. The names or the NSC No. of the 1429 compounds.

list("cell.line")

a list containing two character vector components: Sample the names of the 60 cell line which were analysed, and Class the phenotypes of the 60 cell lines.

Details

The data come from a pharmacogenomic study (Szakacs et al., 2004) in which two kinds of measurements acquired on the NCI-60 cancer cell lines are considered:

• the expression of the 48 human ABC transporters measured by real-time quantitative RT-PCR for each cell line;

• the activity of 1429 drugs expressed as GI_{50} which corresponds to the concentration at which the drug induces 50\% inhibition of cellular growth for the cell line tested.

The NCI- 60 panel includes cell lines derived from cancers of colorectal (7 cell lines), renal(8), ovarian(6), breast(8), prostate(2), lung(9) and central nervous system origin(6), as well as leukemias(6) and melanomas(8). It was set up by the Developmental Therapeutics Program of the National Cancer Institute (NCI, one of the U.S. National Institutes of Health) to screen the toxicity of chemical compound repositories. The expressions of the 48 human ABC transporters is available as a supplement to the paper of Szak?cs et al. (2004).

The drug dataset consiste of 118 compounds whose mechanisms of action are putatively classifiable (Weinstein et al., 1992) and a larger set of 1400 compounds that have been tested multiple times and whose screening data met quality control criteria described elsewhere (Scherf et al., 2000). The two were combined to form a joint dataset that included 1429 compounds.

Value

none

Source

The NCI dataset was downloaded from The Genomics and Bioinformatics Group Supplemental Table S1 to the paper of Szakacs et al. (2004), http://discover.nci.nih.gov/abc/2004_cancercell_abstract.jsp#supplement

The two drug data sets are a companion resource for the paper of Scherf et al. (2000), and was downloaded from http://discover.nci.nih.gov/datasetsNature2000.jsp.

References

Scherf, U., Ross, D. T., Waltham, M., Smith, L. H., Lee, J. K., Tanabe, L., Kohn, K. W., Reinhold, W. C., Myers, T. G., Andrews, D. T., Scudiero, D. A., Eisen, M. B., Sausville, E. A., Pommier, Y., Botstein, D., Brown, P. O. and Weinstein, J. N. (2000). A Gene Expression Database for the Molecular Pharmacology of Cancer. Nature Genetics, 24, 236-244.

Szakacs, G., Annereau, J.-P., Lababidi, S., Shankavaram, U., Arciello, A., Bussey, K. J., Reinhold, W., Guo, Y., Kruh, G. D., Reimers, M., Weinstein, J. N. and Gottesman, M. M. (2004). Predicting drug sensivity and resistance: Profiling ABC transporter genes in cancer cells. Cancer Cell 4, 147-166.

Weinstein, J.N., Kohn, K.W., Grever, M.R., Viswanadhan, V.N., Rubinstein, L.V., Monks, A.P., Scudiero, D.A., Welch, L., Koutsoukos, A.D., Chiausa, A.J. et al. 1992. Neural computing in cancer drug development: Predicting mechanism of action. Science 258, 447-451.

mixOmicsTeam/mixOmics documentation built on Nov. 29, 2024, 2:25 a.m.