Question: How To Produce Directed Graph Of Pathway From A Given Dataset Using Annotation From Kegg?
1
gravatar for Max
8.8 years ago by
Max10
Max10 wrote:

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???

pathway R kegg gene microarray • 2.6k views
ADD COMMENTlink modified 8.7 years ago by Larry_Parnell16k • written 8.8 years ago by Max10
1

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

ADD REPLYlink written 8.8 years ago by Michael Dondrup46k

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.

ADD REPLYlink written 8.8 years ago by Max10
3
gravatar for Giovanni M Dall'Olio
8.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

There are many alternatives:

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

ADD COMMENTlink written 8.8 years ago by Giovanni M Dall'Olio26k
2
gravatar for Chris Miller
8.8 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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

ADD COMMENTlink written 8.8 years ago by Chris Miller21k
2
gravatar for Larry_Parnell
8.8 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 8.8 years ago by Larry_Parnell16k
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