Figure 4

Summary of experimental datasets and their overlap with iNJ 661 and the iNJ 661 gene deletion studies. OptGro refers to the dataset described in [23], ConstExp refers to the dataset described in [29], and Infect describes the dataset in [30]. ^ denotes the subset of genes from the experimental dataset contained in iNJ 661. iNJ 661 represents the 661 genes in the reconstruction. iNJ 661 optimal growth represents the subset of genes required for optimal growth with the original objective function. iNJ 661 optimal growth* represents the subset of genes required for optimal growth with the objective function expanded to include vitamins and cofactors. iNJ 661 alternative objective represents the set of genes required for optimal growth using the objective function constructed based on the ConstExp dataset. Panel A: The Venn diagram shows the overlap between the different experimental gene expression datasets. The accompanying chart summarizes the total number of genes in each dataset and how many of those genes are found in the iNJ661 reconstruction. Panel B: Series of Venn diagrams summarizing the results for the gene deletion studies carried out of iNJ 661 compared to the experimental gene expression datasets.