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. The list was cross referenced with the PEC database to ensure that all genes were considered unessential. Once completed, the list was narrowed down to reactions which used only two genes. Finally, the two genes were deleted in the model and their resulting growth rate was recorded. This was done to clarify that the growth rate was either zero or incredibly low (as predicted by the model). 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).