Accessing NCI-DREAM Cancer Genomics Data

The NCI-DREAM data set is a subset of the data reported in Daemen et al.^{23 (link)} Genome copy number data has been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/), hosted at the EBI (accession numbers EGAS00000000059 and EGAS00001000585). Gene expression data for the cell lines were derived from Affymetrix GeneChip Human Genome U133A and Affymetrix GeneChip Human Exon 1.0 ST arrays. Raw data are available in ArrayExpress (http://www.ebi.ac.uk/arrayexpress), hosted at the EBI (accession number E-TABM-157 and E-MTAB-181). RNA-seq and exome-sequencing data can be accessed at the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/), accession number GSE48216. Genome-wide methylation data for the cell lines are also available through GEO, accession number GSE42944. Scripts to perform the wpc-index and resampled Spearman scoring can be found on the DREAM website (http://www.the-dream-project.org/). Source code for the Bayesian multitask MKL method can be found as Supplementary Software.

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Costello J.C., Heiser L.M., Georgii E., Gönen M., Menden M.P., Wang N.J., Bansal M., Ammad-ud-din M., Hintsanen P., Khan S.A., Mpindi J.P., Kallioniemi O., Honkela A., Aittokallio T., Wennerberg K., Collins J.J., Gallahan D., Singer D., Saez-Rodriguez J., Kaski S., Gray J.W, & Stolovitzky G. (2014). A community effort to assess and improve drug sensitivity prediction algorithms. Nature biotechnology, 32(12), 1202-1212.

Publication 2014

GeneChip Human Genome U133A GeneChip Human Exon 1.0 ST

Cell lines Dream European Exon Gene expression Genechip Genome Human Human genome Methylation Rna seq

Corresponding Organization :

Other organizations : Howard Hughes Medical Institute, Boston University, Oregon Health & Science University, Aalto University, Helsinki Institute for Information Technology, European Bioinformatics Institute, Wellcome Trust, Columbia University, Institute for Molecular Medicine Finland, University of Helsinki, National Cancer Institute, National Institutes of Health, IBM (United States)

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Variable analysis

independent variables

Genome copy number data
Gene expression data from Affymetrix GeneChip Human Genome U133A and Affymetrix GeneChip Human Exon 1.0 ST arrays
RNA-seq and exome-sequencing data
Genome-wide methylation data

dependent variables

Measured outcomes

control variables

Positive and negative controls (not explicitly specified)

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