FEV_KEGG.Experiments.21 module

Context

Similar to 20, where results seemingly showed very diverse metabolism. Possible reasons might have been a poor choice of example organisms or not enough organisms per group. These reasons can be mitigated by this experiment, up to the amount of real-world organisms available in KEGG. A small common ‘core metabolism’ is expected to be found, except for symbionts.

Question

Taking a complete set of organisms, forming a group (Brachyspirales, Order) and a super group (Spirochaetes, Class) of organisms, how many functions occur in the majority network of the group, but not in the majority network of the super group? For varying majority-percentages.

Method

Similar to 20, only different sets, complete sets, and ‘how many?’ instead of ‘which?’ functions. - Create a group of all organisms of Order Brachyspirales to be found in KEGG. - Create a super group of all organisms of Class Spirochaetes to be found in KEGG, including the same organsims as the group of Order. - REPEAT for varying majority-percentages: - Calculate majority substance-ec graphs for both groups. Leaving only EC numbers which occur in all organisms of the group. - Calculate the difference of the two sets of majority EC numbers, leaving only the EC numbers which occur in Order majority, but not in Class majority. - Print the amount of EC numbers and their percentage of all EC numbers in Order, ie. how many of the EC numbers in Order do not exist in Class majority.

Result

269/295 -> 91.2% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 100% majority for both
249/295 -> 84.4% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 90% majority for both
268/328 -> 81.7% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 80% majority for both
272/342 -> 79.5% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 70% majority for both
271/354 -> 76.6% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 60% majority for both
269/380 -> 70.8% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 50% majority for both
200/380 -> 52.6% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 40% majority for both
146/389 -> 37.5% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 30% majority for both
 78/395 -> 19.7% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 20% majority for both
 36/425 ->  8.5% of EC numbers in Brachyspirales are new, compared to Spirochaetes majority @ 10% majority for both

Conclusion

This group (Brachyspirales) is even more diverse than Enterobacteriales in 20. It is, therefore, unlikely that a poor selection of example organisms caused the results in 20. It might still be the case that KEGG only contains poor representatives of the real group, which can never be ruled out.

Even though the threshold of majority decreases the same for group and super group, the size of the majority network is rather constant for Brachyspirales. The size of the majority network for Spirochaetes, however, seems to increase quicker, yet linearly, with decreasing majority threshold. This indicates an even greater diversity in the super group Spirochaetes.