The files below are hierarchy trees for all organisms of the WIT database (as described in the article Subnetwork hierarchies of biochemical pathways ). These are PNG (Portable Network Graphics) files of sizes less than 70kbytes. The whole-cell network trees for B. burgdorferi and M. pneumoniae have substance names, for metabolic network trees these and T. pallidum and C. pneumoniae are likewise annotated. Looking at the trees from right to left, you can see in what order the subnetworks breaks. By placing a vertical cut you can see what networks are connected at a specific time. Source code and instructions how to run the programs can be obtained here.

Aeropyrum pernix [metabolic] [whole-cell ] Archaeoglobus fulgidus [metabolic] [whole-cell ]
Methanobacterium thermoautotrophicum [metabolic] [whole-cell] Methanococcus jannaschii [metabolic] [whole-cell ]
Pyrococcus furiosus [metabolic] [whole-cell] Pyrococcus horikoshii [metabolic] [whole-cell ]
Aquifex aeolicus [metabolic] [whole-cell ] Chlamydia pneumoniae [metabolic] [whole-cell ]
Chlamydia trachomati [metabolic] [whole-cell ] Synechocystis sp. [metabolic] [whole-cell ]
Porphyromonas gingivalis [metabolic] [whole-cell ] Mycobacterium bovis [metabolic] [whole-cell ]
Mycobacterium leprae [metabolic] [whole-cell ] Mycobacterium tuberculosis [metabolic] [whole-cell ]
Bacillus subtilis [metabolic] [whole-cell ] Enterococcus faecalis [metabolic] [whole-cell ]
Clostridium acetobutylicum [metabolic] [whole-cell ] Mycoplasma genitalium [metabolic] [whole-cell ]
Mycoplasma pneumoniae [metabolic] [whole-cell ] Streptococcus pneumoniae [metabolic] [whole-cell ]
Streptococcus pyogenes [metabolic] [whole-cell ] Chlorobium tepidum [metabolic] [whole-cell ]
Rhodobacter capsulatus [metabolic] [whole-cell ] Rickettsia prowazekii [metabolic] [whole-cell]
Neisseria gonorrhoeae [metabolic] [whole-cell ] Neisseria meningitidi [metabolic] [whole-cell ]
Campylobacter jejuni [metabolic] [whole-cell ] Helicobacter pylori [metabolic] [whole-cell ]
Escherichia coli [metabolic] [whole-cell ] Salmonella typhi [metabolic] [whole-cell ]
Yersinia pestis [metabolic] [whole-cell ] Actinobacillus actinomycetemcomitans [metabolic] [whole-cell ]
Haemophilus influenzae [metabolic] [whole-cell ] Pseudomonas aeruginosa [metabolic] [whole-cell ]
Treponema pallidum [metabolic] [whole-cell ] Borrelia burgdorferi [metabolic] [whole-cell ]
Thermotoga maritima [metabolic] [whole-cell ] Deinococcus radiodurans [metabolic] [whole-cell ]
Emericella nidulans [metabolic] [whole-cell ] Saccharomyces cerevisiae [metabolic] [whole-cell ]
Caenorhabditis elegans [metabolic] [whole-cell ] Oryza sativa [metabolic] [whole-cell]
Arabidopsis thaliana [metabolic] [whole-cell ]

Petter Holme
April, 2002