Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models
Fig 5
(A): Reaction content. Classical multidimensional scaling was performed on the reaction content of all de novo reconstructions; each reconstruction is represented by a point (grey/black or colored by database for emphasis). Thus, this analysis focuses exclusively on the genetically supported features of each reconstruction. Apicomplexan parasites (colored by database) and all other gut pathogens (black points) are highlighted. (B): Reaction content with alternative color scheme. Parasites that invade red blood cells (triangles, Plasmodium and Babesia) or can replicate extracellularly (circles) are highlighted; all other parasites are in lighter grey squares. (C): Important variables for the classification of gut pathogens. We performed a random forest classification to distinguish organisms that are considered gut pathogens from other organisms in ParaDIGM (AUC = 0.98 and an out-of-bag error rate of less than 8%). Important variables with a difference in occurrence score of 1 were present in 100% of gut pathogens and 0% of other organism’s reconstructions and those with a score of -1 were present in 100% of non-gut pathogens and 0% of gut pathogen’s reconstructions. (D): Transporter profile. Again, parasites that invade red blood cells (triangles) or can replicate extracellularly (circles, like the kinetoplastids and Giardia, among others) are highlighted, with all other parasites are in lighter grey squares. Red blood cell-invading parasites cluster.