Question: KEGG pathway visualization AND Cytoscape
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gravatar for pixie@bioinfo
14 months ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

Hello, I have been trying to visualize KEGG pathways for a group of metabolites (in Tomato). I am getting mappings to 34 different pathways, many of which have common metabolites. My supervisor wants me to combine the individual pathways in a global map so that we can color code the nodes and see the flow of information. I could not find any resource which does that. I used Cytoscape to import the KGML files from KEGG and tried to merge the pathway-networks, but the layouts are getting completely altered which is making it difficult to visualize the pathways. ANy help on this or any other resource is greatly appreciated.

kegg • 744 views
ADD COMMENTlink modified 14 months ago by sgoetz12320 • written 14 months ago by pixie@bioinfo1.4k

Excellent question, I recently did the same by hand, I did not found anything to automate it. I just identify the related genes by using a venn diagram and reading tens of papers to justify the joined pathways and correlations. If you find a useful tool please told me :)

ADD REPLYlink written 14 months ago by Buffo1.8k
0
gravatar for sgoetz123
14 months ago by
sgoetz12320
Valencia
sgoetz12320 wrote:

Hello. You could try the Paintomics tool which generates a network of KEGG pathways and allows you to also add expression and other omics data. See here for more information: [http://www.paintomics.org/]

ADD COMMENTlink modified 13 months ago • written 14 months ago by sgoetz12320
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