How To Produce Directed Graph Of Pathway From A Given Dataset Using Annotation From Kegg?

Question

[Max]

Let say i have a gene expression microarray data (e.g gasch)..how can I produce a directed graph of pathway associated with the dataset using the annotation from KEGG??..

I have found a R-package called PathRanker but it seem the instruction are to complex for me to understand and the result that i get aren't similar with the paper...

can someone explain to me and help me with the R package???

[Michael]

Can you explain a bit about your difficulties with the package?

[Max]

I tried to run the package using the manual provided but it seems that the results that i get are not similar with the paper therefore its hard for me to analyze the result without proper reference.

Answer 1

[Giovanni M Dall'Olio]

There are many alternatives:

• KEGGgraph for R
• the KGML reader plugin for Cytoscape

What is more important, remember to check the results manually.

Answer 2

[Chris Miller]

I believe Cytoscape has some plugins for this sort of thing. (one such plugin)

Answer 3

[Larry_Parnell]

It is also important to keep in mind that many biochemical pathways are bi-directional - they can be transited in both directions depending on several factors, including concentration of reactant(s) and product(s). We tend to think that higher gene expression = more protein, more enzyme and this = more product from the biochemical reaction. The enzyme concentration may not be rate-limiting and so higher gene expression may have little to zero effect on the pathway flux.