Is it possible that a plant has a KO cathegory associated with human disease?

Question

[aboutmb]

Hi, I'm working on RNA-seq analysis of a non-model plant and I need to generate a KO list to use iPath2. I used "Kegg Mapper" to obtain a KO annotation, but I got 20% from Human Disease - even it having been selected just Solanaceae. How can I deal with these? If anyone can help me, I'll really appreciate that.

Thank you!

Answer 1

[Philipp Bayer]

I've actually run into the same thing today when I was wondering why my clover had Diabetes - the Kegg Pathways are split into six level A groups from ko00001.keg, which in turn are split into several subgroups:

Metabolism
Genetic Information Processing
Environmental Information Processing
Cellular Processes
Organismal Systems
Human Diseases

K-numbers can be in several of those at once, for example, my clover has K01580, which is part of "Butanoate metabolism PATH:ko00650]" which is part of "Carbohydrate metabolism", which sounds alright.

However, K01580 is also part of "4940 Type I diabetes mellitus [PATH:ko04940]" in the "Endocrine and metabolic diseases" under "Human Diseases", since the same pathways are employed in diseases in humans.

I'd just ignore everything in Human Diseases.

[aboutmb]

Thank you so much! I appreciate your attention!

Answer 2

[Benn]

Yes, it is possible that many genes are associated with human diseases. There is a bias in these annotation databases, since most research is done with human diseases.

How to deal with it? Use your common sense I would say. A computer does not understand the difference between human or plant genes, but you as a researcher do!