Instructions for using code associated with “RadSigBench: A Framework for Benchmarking Functional Genomics Signatures of Cancer Cell Radiosensitivity” Authors: John O’Connor, Ian Overton, and Stephen McMahon
The purpose of the paper was to implement gene signatures of radiosensitivity and test them in two datasets, namely the NCI60 and the CCLE. The 3 scripts (which should be run in order for each dataset) provided here were used for:
• Cleaning/matching radiosensitivity and expression data
• Generating and testing random signatures
• Testing published signatures and producing comparison plots
NCI60 – Radiosensitivity data (SF2) for this dataset comes from the clonogenic assay and was taken from Table 1 and Table 4 of “Eschrich et al. International Journal of Radiation Oncology Biology Physics 2009; 75:497–505”. This is included in the repository.
CCLE – Radiosensitivity data (MID) comes from a high throughput assay and is labelled as “AUC” in the “Supplemental Data 1” from “Yard et al. A genetic basis for the variation in the vulnerability of cancer to DNA damage. Nat. Commun. 2016; 7:11428”. This is not included in the repository and will have to be downloaded from the publication and renamed to: “Supplementary_Data_1_Yard_et_al.csv” and put in the raw data folder.
NCI60 – This data is from GSE32474 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32474). It is downloaded and unzipped within the R code for cleaning the NCI60 data.
CCLE – This data is in the “CCLE_Expression_2012-09-29.res” file and needs to be downloaded from https://depmap.org/portal/download/. It can be found under the “All Downloads” tab on the left of the screen. This needs to be added to the “raw_data” folder.