I am having a list of genes and I would like to acquire the genes that are found in the previous and the next reaction in each pathway from every of the genes in the list.
I'm looking for ways to do that in kegg and I could just include all the genes that exist in the previous and the next nodes, but the way the pathways are organized complicates this task.
For instance I'm looking at which genes PPAP2B affects, which exists in a few pathways. I take a look at a pathway where PPAP2B exists and the node is comprised by an EC number which contains many ko numbers which in turn contain many genes. This doesn't allow me to seclude PPAP2B in the pathway to let me understand by which genes specifically is affected and which in turn it affects. Or rather I haven't understood the way pathways are organized.
Is there a way of doing what I am asking? If yes, is there an automated way or I must do it manually?