Reproducible Bioinformatics Analysis Pipeline

Annotated R code (in Sweave format) to reproduce all of the analysis in this paper is available from our website [57 ]. The CGP gene expression data are available from ArrayExpress under accession number E-MTAB-783. The IC₅₀ data for the drugs is available from the CGP website [52 ]. The docetaxel data are available from GEO under accession numbers [GEO:GSE349] and [GEO:GSE350]. The cisplatin data are available from ArrayExpress under accession number E-GEOD-18864. The bortezomib data are available from GEO under accession number [GEO:GSE9782]. The erlotinib data are available from GEO under accession number [GEO:GSE33072]. Complete details and R code showing how to acquire and preprocess all of these data, as well as the associated clinical data are available in Sweave format on our website.

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Geeleher P., Cox N.J, & Huang R.S. (2014). Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biology, 15(3), R47.

Publication 2014

Bortezomib Cisplatin Docetaxel Drugs Erlotinib Gene expression

Corresponding Organization :

Other organizations : University of Chicago

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Protocol cited in 23 other protocols

Variable analysis

independent variables

IC50 data for the drugs

dependent variables

CGP gene expression data
Docetaxel data
Cisplatin data
Bortezomib data
Erlotinib data

control variables

None explicitly mentioned

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