I have a question regarding the statistics depicted in KEGG ontology term depiction. When I annotate assembled transcripts in RNA-seq experiment or predicted genes in Meta-genomic experiments, I often do pathway annotation with KEGG IDs (i.e, KO terms).
Now when we give the statistics of the KO annotation, We write it as
Cellular transport = X
Metabolism=Y so on.
This is where my question is, This value (X or Y) should depict what ?? The number of KO IDs under that category or number of sequences bearing KO IDs from that category which of these makes more sense ???