The majority of essential gene experiments in the literature involve single gene knock outs. However, our model has a unique ability to predict what combinations of gene deletions will be lethal. However it is important to determine how accurate the model is in determining these multiple gene deletion results. For this reason, the Model Validation attempts to answer the question; is a series of dual deletions which cause death in our model accurately reflected in vivo?

In order to achieve a series of double deletions and accurately predict the model’s effects in vivo, MATLAB was used to produce a program which could identify genes which worked in combination. The DualDeletionTest.m file is designed to slowly delete reactions one at a time to determine which reactions are essential to the cell. The data which was saved, was the genes (listed by blattner number) which catalyze the reaction. This list could then be used to find essential reactions which could be catalyzed by two different genes. Once these genes were identified, they were cross referenced with the PEC database to ensure that they were considered unessential by single gene knockout data. Following this, two sets of genes were selected to perform wetlab experiments with. These were CysM and CysK, as well as MetH and MetD. (To see data produced by DualDeletionTest.m and the processed data click here).