I have a simple question (or maybe not), about which are the criteria to decide if a particular KEGG pathway in a particular organism I am working with, is or is not complete.
After running GhostKOALA I have these data:
Reconstruct Pathway Reconstruct Brite Reconstruct Module
The section Module of KEGGs is quite descriptive about this issue, and gives the information of complete or incomplete block. But not all the Path are associated to modules, etc... so the information about the completeness is not always available. Furthermore, for specific pathways such as 04012 ErbB signaling pathway for example, there is not module associated to tell me that the path is complete...so how do you do in such cases?
Or why if the KO in Reconstruct Pathway seems to have all the KO associated to a gene, in Reconstruct Module there are different in numbers or lacks some gene ids?
I hope someone could answer to this. Thanks in advance.