Question: Merging Kegg Pathways
4
gravatar for Sudeep
7.2 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

Dear All, I have a set of some what related KEGG pathways (glycolysis and tca cycle for example). Are there any tools available that can merge these pathways (say if I give KGML files of these pathways as input) ?. I came across a few tools that can visualize and manipulate individual pathways, but couldn't find anything that can merge them.

Thank you in advance


edit:

Quick fix that I found: Looks like VisANT merges pathway files. I tried uploading TCA cycle and Glycolysis pathway KGML files and VisANT somehow connects one to another

pathway genes kegg • 4.8k views
ADD COMMENTlink modified 3.1 years ago by kandoigaurav120 • written 7.2 years ago by Sudeep1.6k
4
gravatar for Michael Schubert
7.2 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

KeggConverter can do this, for instance.

Bear in mind, however, that the KGML is generally of lower quality than the graphical representations (missing information, orphan nodes, etc).


edit: Another possibility is to translate the KGML to SBML with KEGGTranslator and then merge the models using e.g. SemanticSBML. You might want to go the route via SBML anyway because it is a standard open format and the software support is better than for the KGML.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Michael Schubert6.9k

Thank you ... but the link in the paper to the download page appears to be dead. I found this pathvisio project (http://www.pathvisio.org/wiki/KeggConverter) with same name but I am not sure if it is the same one.

ADD REPLYlink written 7.2 years ago by Sudeep1.6k
1

You are right. The converter in PathVisio seems to just do KGML->GPML. I updated the answer.

ADD REPLYlink written 7.2 years ago by Michael Schubert6.9k
2
gravatar for ff.cc.cc
7.2 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

"Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data".

There are a few plugins available for importing KGML files as cytoscape networks (e.g. look for kgmlreader, genoscape...).
So, the user can import a couple of kegg pathway as separate networks and then merge them with the "merge networks" tools.

Good luck!

ADD COMMENTlink written 7.2 years ago by ff.cc.cc1.3k

Thank you for your suggestion

ADD REPLYlink written 7.2 years ago by Sudeep1.6k
2
gravatar for kandoigaurav
3.1 years ago by
kandoigaurav120
United States
kandoigaurav120 wrote:

A pretty old post, but thought it might help the future users. I wrote this little R script using KEGGgraph, tkWidgets and some base R graph functions.

library(tkWidgets)
library(KEGGgraph)
library(KEGG.db)

pathways = list.files(pattern="*.xml")
for (i in 1:length(pathways)) assign(pathways[i], parseKGML2Graph(pathways[i],expandGenes=TRUE))
rm(i);rm(pathways)
pathways<-objNameToList(objects(), parent.frame())
merged <- ugraph(mergeKEGGgraphs(pathways, edgemode = "directed"))

This will give you an undirected graph (because of ugraph() ). If you wish to retain the original directed graph, just replace the last line with the following:

merged <- mergeKEGGgraphs(pathways, edgemode = "directed")

Hope that helps!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by kandoigaurav120

Thanks a bunch. That was all I was looking for. I had one trouble though. My global environment has a lot of other values and datasets. So this command pathways<-objNameToList(objects(), parent.frame()) those other files. I have clear global environment before running the above code snippet. I am new with R so help would be appreciated.

ADD REPLYlink written 2.3 years ago by urwa0
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