This query allows to evaluate gene, reaction or TF essentiality, in a specified growth media.

The output is a table of genes, reactions or TFs, whose deletion is predicted to lead to biomass production flux levels below 1% of that of the wild-type strain, as defined by COBRApy .

The exact biomass production flux predicted by in silico deletion of the indicated gene/reaction/TF is displayed. Although intuitively KO (KnockOut) and UE (Under-Expression)=0 appear to be the same operation, the simulation tool interpret them as different things. The difference lies only in reactions for catalised by multiple enzymes with the same function. When this is the case, in the "KO" simulation, the deletion of a gene is simulated as having no impact on the reaction flux, as the other isoenzymes are supposed to fully replace the absence of the deleted one. In the "UE=0.00" simulation the deletion of a gene leads to a decrease in the corresponding reaction flux, inversely proportional to the number of isoenzymes (e.g. if there are 3 isoenzymes capable of catalysing a reaction, the deletion of the gene under analysis will lead to a 33% reduction of the reaction flux).