FEV_KEGG.Experiments.27 module

Context

Some organisms belong to an ‘unclassified’ taxon. They are hard to compare against other taxa.

Question

How does excluding ‘unclassified’ Archaea change the number of EC numbers new to Thaumarchaeota? How does it change the number of neofunctionalised EC numbers?

Method

• get NCBI taxonomy tree
• get group of organisms ‘Archaea/Thaumarchaeota’
• get supergroup of organisms ‘Archaea’
• calculate new EC numbers occuring in group’s core metabolism compared to supergroup’s core metabolism
• calculate neofunctionalised EC numbers in group’s core metabolism
• repeat all, but excluding taxa containing ‘unclassified’ in both group and supergroup
• repeat all, but excluding taxa containing ‘Nitrososphaeria’ in both group and supergroup

Result

taxon exception: None
new EC numbers: 110
neofunctionalised EC numbers: 11

taxon exception: unclassified
new EC numbers: 172
neofunctionalised EC numbers: 16

taxon exception: Nitrososphaeria
new EC numbers: 114
neofunctionalised EC numbers: 9

Conclusion

Excluding ‘unclassfied’ organisms has a significant impact on core metabolism. This might be due to 1) reduced number of organisms, leading to higher chances of a consensus in metabolism 2) the unclassified organisms here have an unusual metabolism

Excluding a sub-group of the same size (4 organisms), however, does not yield significant changes. This implies a strong preference for option 2) above.