As for the molecular function category, unigenes with binding and catalytic activity formed the largest groups.
(b) Performance evaluation in the Molecular Function category.
In the Molecular Function category, performance may be considered accurate.
For molecular function category, metabolic process, catalytic activity, and cofactor binding were the top abundant subcategories.
For the Molecular function category, the most highly represented genes were associated with "binding" and "catalytic activity".
This resulted in 188 easy and 343 difficult targets in the Molecular Function category and 247 easy and 340 difficult targets in the Biological Process category.
As for the Molecular function category, genes involved in "(metal) ion binding" and "DNA binding" were highly present in the UI (Supplemental Fig. 6).
For example, in the Molecular Function category, 79% of proteins had one leaf term, 16% had two leaf terms, and so on.
Performance was generally similar in the Molecular Function category, but in the Biological Process category we observed high prediction accuracy for prokaryotic targets.
In the Molecular Function category, proteins with "protein binding" as their only leaf term were excluded from the analysis because the protein binding term was not considered informative (results that include those proteins are presented in Supplementary Fig. 3).
With few exceptions, the same methods that performed well for the Molecular Function category also performed well in the Biological Process category; however, their overall performance in the latter category was inferior.
