GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Fig 5
Assessment of GPRuler performance in reconstructing GPRs of ground truth models.
Panel A shows a summary of GPRuler performance highlighting the percentage of the automatically reconstructed rules in each ground truth models (labelled as “Automatic” and coloured in dark yellow) against those that cannot be correctly reconstructed unless a subsequent curation by the user (labelled as“Not automatic” and coloured in light blue). The mosaic plots below show in B) HMRcore, C) Recon3D, D) Yeast 7 and E) Yeast 8 model the frequency of “Automatic” GPR rules as proportional to the size of internal rectangles. The rectangle portions having low transparency corresponds to the “Not automatic” rules. GPRs are classified according to the type of relationships established among genes involved in reaction catalysis as “No gene”, “One gene” and “Multi gene”. In the “Multi gene” class, the three subclasses “OR”, “AND” and “Mixed” are also represented. On the horizontal side of each mosaic plot, the proportion of “No gene”, “One gene” and “Multi gene” Automatic GPR rules in each model is reported. On the vertical side of each mosaic plot, the same information is reported for the three classes “OR”, “AND” and “Mixed” over the percentage of Automatic Multi gene rules.