CancerSSDTs

Published: 13 March 2024| Version 1 | DOI: 10.17632/fpwtnn9yp8.1
Contributors:
mehdi Dehghan Manshadi,
,
,
,

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".

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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".

Institutions

Shiraz University

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