How to limit KAAS pathway results to certain species?

Question

[xie186]

I'm working on a dataset in an insect species. I was using KAAS to annotate the genes. In the parameter for "GENES data set", I only selected some species from insects.

But in the results, the Pathway Mapping gave pathways definitely human specific, E.g. "Coronavirus disease - COVID-19". In this pathway, there is one KO K02580. This KO belongs to many pathways. One of them is "Coronavirus disease - COVID-19". My question is:

Is there a way that I can exclude some of the pathways that we know definitely not related to insects? Any suggestions? Thanks.

[adhamzul]

Hi omicsgeek!

I am facing the same problem as you. As practice for using KAAS, I annotated the E. coli K-12 MG1655 sequences using RAST and used KAAS to determine the metabolic pathways of the genes. I selected only the exact same organism for the GENES data set, but I still get genes that are not related to E. coli.

I was wondering if you found out any ways to overcome this problem.

Regards, Adham.

Answer 1

[xie186]

Yes I do. This is what I did:

1. In the webpage of KAAS, I'll get a list of species I would like to limit the pathways to. eg. dme, dya.
2. Download the pathways for the species you selected using the link below:

http://rest.kegg.jp/link/pathway/dme

http://rest.kegg.jp/link/pathway/dya

In the second column, you will see the IDs. I put an example down below here: dme:Dmel_CG10160 path:dme00010

The idea is that dme00010 and ko00010 are referencing to the same pathway:

https://www.genome.jp/entry/dme00010

https://www.genome.jp/entry/ko00010

So you can only include that pathways that are in the selected species based on the IDs without letters prefixed.

Hope this helps.