FEV_KEGG.Experiments.34 module

Context

Extending 32 by removing the outdated EC numbers found in 33.

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)? Not taking into account outdated/faulty data.

Method

  • extract EC numbers from Oh et al. (2007) by hand
  • remove outdated EC numbers
  • 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%:    30    311    237
 90%:    9    332    263
 80%:    3    338    269
 70%:    3    338    270
 60%:    2    339    270
 50%:    2    339    270
 40%:    2    339    272
 30%:    2    339    272
 20%:    2    339    273
 10%:    2    339    276
  1%:    1    340    285

Conclusion

Beginning with 80% majority there are less than 4 EC numbers unexplainably missing in our core metabolism. This seems to imply that our approach is correct and useful, under the constraints imposed by KEGG’s completeness and correctness.