IDEA is an in silico framework for systematic pre-clinical screening of potential therapeutic compounds based on the integration of disease gene expression profiles, drug treatment profiles, and patient time-to-event survival information.



Readme: Description about format and commands for the above program.

Drug Treatment Profile Sample dataset: Pre-processed and normalized "up" and "dn" drug treatment profiles derived from CMap MCF7 data. The sample data contain "up" and "dn" drug treatment profiles for three drugs.

Gene Expresion Profile Sample dataset: Gene expression profiles for 50 breast cancer tumor samples. The sample data are derived from the METABRIC data by Curtis et al.

Patient Sample Clinical Information: The clinical information for 50 breast cancer patients. The sample data are derived from the METABRIC data by Curtis et al.

DRS Profiles for the Sample dataset: The DRSs of the three drugs (DTP sample data) in the 50 tumor samples (GEP sample data)

generateDRS.r: R code used to generate DRS profiles from MCF7 drug treatment profiles

survival_analysis_DRS.r: R code used to implement survival analysis using DRS profiles and clinical information as covariates



[1] IDEA: Integrated Drug Expression Analysis -- Integration of gene expression and clinical data for the identification of therapeutic candidates. Ung MH, Varn FS, Cheng C. CPT:Pharmacometrics and Systems Pharmacology. 2015. Under Review.


Chao Cheng