Supplementary Dataset DS1: cMap Drugs prototype ranked lists
Compressed tab delimited txt file containing the ‘prototype ranked lists’ of genes for all the drug contained in the connectivity map dataset, computed as described in Iorio et al, PNAS 2010.
Make sure you have the following libraries installed (all available on the CRAN repository):
To install them use the following command from the RStudio console:
library.name] with each of the library names listed above, in turn.
Once uncompressed, the content of this folder and its sub-folders should not be changed. Files in the OUTPUT subfolder (initially empty) can be moved and/or deleted.
To set the working directory to IorioEtAl_R_code_and_objects use the following command from the RStudio console:
[path] with the path of the IorioEtAl_R_code_and_objects directory.
Ready to go!
To reproduce results and figure presented in our manuscript execute the commands contained in the following pipelines:
 Lamb J. The Connectivity Map: a new tool for biomedical research. Nature Reviews Cancer. 2007;7(1): 54–60.
 Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, et al. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proceedings of the National Academy of Sciences. 2010;107(33):14621.
 Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J. Transcriptional data: a new gateway to drug repositioning? Drug Discovery Today. Elsevier Ltd; 2013 Apr 1;18(7-8):350–7.
 Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. Nature Publishing Group; 2012 Mar 20;483(7391):570–5.