Define genes relation in KEGG pathway and thier reaction

Question

[shawin]

How can we define the genes relation in a specific pathway and their reaction. the link bellow is matlab method to do some operation on KEGG but it does not provide a method to detect the genes relation and reaction

http://uk.mathworks.com/help/bioinfo/examples/connecting-to-the-kegg-api-web-service.html#zmw57dd0e15301

Answer 1

[seta]

You may try KAAS to automatically KEGG annotation and assign KO to the related genes.

Answer 2

[svlachavas]

Also if you have a specific group of genes(i suppose you want for the last KEGG native view for "Fatty acid Degredation") and you can play with R, you can use the pathview R package which has wonderful visualizations, as also alternative figures with Graphviz showing nodes and type of interaction. Just keep in mind, if you want to validate "appropriately" the relationship of a specific input of genes to a pathway, maybe it is more relevant to perform a topology-based pathway analysis, in order to also see the pertubation progagation in a specific pathway, and not just color the genes of interest found enriched in a pathway.

Best,

Efstathios