CancerSSDTs
Description
CancerSSDTs This repository contains data, codes, and supplementary information used to identify strictly-selective drug targets for 13 cancers. Requirements The following tools are needed: COBRA Toolbox rFASTCORMICS CPLEX v12.9.0 or any CPLEX version compatible with MATLAB. To Obtain Strictly Selective Lethal Sets, Follow the Steps Below: Initialize COBRA toolbox: initCobraToolbox Use rFASTCORMICS to build normal and cancer context-specific models for each tissue. The parameters for this step are provided in BuildCSM.m. Provided models are available in Contex_Specific_Models: BuildCSM.m Use RapidSL to identify single and synthetic lethal drug targets for all cancers. A sample script is provided in RunRapidSL.m. All identified selective and non-selective solutions are available in All_Identified_Synthetic_Lethal_Non_Selective: RunRapidSL.m Use the FindSSDTs.m function to extract strictly-selective drug targets for each cancer. A sample use of this function is provided in IdentifySelectives.m: IdentifySelectives.m All SSDTs identified in this study are available in the Supplementary_File_S1: This repository represents the data related to the following submitted manuscript: Manshadi et al.,"Higher order synthetic lethals are keys to minimizing cancer treatment effects on normal cells".
Files
Steps to reproduce
CancerSSDTs This repository contains data, codes, and supplementary information used to identify strictly-selective drug targets for 13 cancers. Requirements The following tools are needed: COBRA Toolbox rFASTCORMICS CPLEX v12.9.0 or any CPLEX version compatible with MATLAB. To Obtain Strictly Selective Lethal Sets, Follow the Steps Below: Initialize COBRA toolbox: initCobraToolbox Use rFASTCORMICS to build normal and cancer context-specific models for each tissue. The parameters for this step are provided in BuildCSM.m. Provided models are available in Contex_Specific_Models: BuildCSM.m Use RapidSL to identify single and synthetic lethal drug targets for all cancers. A sample script is provided in RunRapidSL.m. All identified selective and non-selective solutions are available in All_Identified_Synthetic_Lethal_Non_Selective: RunRapidSL.m Use the FindSSDTs.m function to extract strictly-selective drug targets for each cancer. A sample use of this function is provided in IdentifySelectives.m: IdentifySelectives.m All SSDTs identified in this study are available in the Supplementary_File_S1: This repository represents the data related to the following submitted manuscript: Manshadi et al.,"Higher order synthetic lethals are keys to minimizing cancer treatment effects on normal cells".