Installation

Source code and supplementary data

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.
SuppDataset_SD1_DRUG_PRLS_txt.zip

How to reproduce results and figures presented in the manuscript?

To start:

Make sure you have R installed. You can download it from here
We strongly recommend to install and use the RStudio interface to R, downloadable from here

Required libraries:

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:

install.packages(“[library.name]”)

replacing [library.name] with each of the library names listed above, in turn.

Working directory creation:

Download and unzip the following compressed folder: IorioEtAl_R_code_and_objects.zip or from GitHub

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.

Working directory setup:

To set the working directory to IorioEtAl_R_code_and_objects use the following command from the RStudio console:

setwd(‘[path]/IorioEtAl_R_code_and_objects’)

replacing [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:

Network guided iterative connectivity mapping pipeline

Pipeline for predictive ability validation through the signature reversion paradigm

References:

[1] Lamb J. The Connectivity Map: a new tool for biomedical research. Nature Reviews Cancer. 2007;7(1): 54–60.

[2] 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.

[3] 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.

[4] 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.

iNRG_cMAP