Hi,
I am trying to extract the pathway level information from different cancer pathways. I need to get the genes involved in all the sub pathways,
For example: Considering the NSCLC pathway (hsa05223 - non-small cell lung cancer), there are different types of pathways inside them; like, Calcium -signaling pathway, MAPK pathway etc. I want to get the list of those genes for studying the pathway cross talk.
Can anyone know, how to get those list?
Erm, KEGG is supposed to be non-hierarchical. Are you sure there actually are any subpathways in kegg?
If you want the pathway to gene maps, this is trivial to do in kg (
pip install kg
):See https://github.com/endrebak/kg for more
By sub pathway, I meant those (example: signaling) pathways which are mentioned in a cancer pathway.
To get pathway list for genes, submit the fasta file in KEGG Automatic Annotation Server (KAAS).