FEV_KEGG.Experiments.32 module

Context

As in the experiments before, the set of EC numbers predicted by our approach is to be compared with the set predicted by the approach of Oh et al. (2007).

Question

Does the consensus/majority graph approach to core metabolism yield a similar set of EC numbers as the approach of Oh et al. (2007)?

Method

  • extract EC numbers from Oh et al. (2007) by hand
  • remove EC numbers with wildcards
  • get group of organisms ‘Bacillus subtilis’
  • REPEAT for varying majority-percentages:
  • calculate EC numbers occuring in group’s core metabolism
  • remove EC numbers with wildcards
  • overlap Oh’s set with ours and print amount of EC numbers inside the intersection and falling off either side

Result

Maj. %    others    both    ours
100%:    135    313    235
 90%:    114    334    261
 80%:    108    340    267
 70%:    108    340    268
 60%:    107    341    268
 50%:    107    341    268
 40%:    107    341    270
 30%:    107    341    270
 20%:    107    341    271
 10%:    107    341    274
  1%:    106    342    283

Conclusion

Even at only 1% (effectively 1 organism) majority, there are many EC numbers predicted by Oh et al., but not occuring anywhere in our model organisms. This may be caused by: 1. EC number is associated with the organism, but not listed in one of KEGG’s hand-drawn pathways. For example 1.13.11.24 is associated with all our 15 organisms, but not present in any pathway. 2. As seen in experiment 30, there may be EC numbers predicted by Oh et al. which are outdated. 3. Oh et al. used a compilation of several sources, some may have predicted EC numbers for B. subtilis which never made their way into KEGG at all, which is our only source.