Question: How To Map Kegg Data - Pathways As Nodes, Compounds As Edges.
2
gravatar for Haji
6.4 years ago by
Haji50
European Union
Haji50 wrote:

Hi. I'm trying to create a network that will present all the pathways found in the KEGG database and the relations between those pathways. I want to represent each pathway as node, and compounds that are shared by two (or more...) pathways as edges. I have not found a tool to perform this task yet. I would be happy to get your advice on this issue. Thanks!

network kegg • 4.4k views
ADD COMMENTlink modified 5.9 years ago by balaji40 • written 6.4 years ago by Haji50
1

What's your input ? a database ? a flat file ? a json file ?

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum118k
1

The global map of pathways is kinda what you want: http://www.genome.jp/kegg/pathway/map/map01100.html

What kind of analysis are you trying to do by generating this map? Are you trying to weigh the pathway nodes by how many genes map to the pathway so you can get a enrichment value for the various pathways?

ADD REPLYlink written 6.4 years ago by Damian Kao15k

Damian, thanks for this link. I've only used "third party" applications to pathway map, so this is a nice addition to the tool box.

ADD REPLYlink written 6.4 years ago by Josh Herr5.6k

Hello Pierre & Damian. Pierre - my initial input is a list of pathways that I wish to map to the network described above. I tried to fetch the related pathways for each of the pathways listed in the KEGG db and use this data to generate a csv file (to use as input for cytoscape). However, I found that information not complete in the KEGG website. Damian - I'm familiar with the global metabolism map. What I want to do is to display the same information, with two main differences: displaying each pathway as a single node (and not few pathways grouped to one edge) and representing each compound, shared by two pathways as edge. What I want to do is to show that the subset of pathways I'm studying compose some kind of module, and are all connected by a certain path length from a specific pathway. Thanks!

ADD REPLYlink written 6.4 years ago by Haji50

Here's a highly relevant paper: http://www.biomedcentral.com/1752-0509/1/29

ADD REPLYlink written 3.3 years ago by glocke01160
1
gravatar for Josh Herr
6.4 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

This is a common question around here. You didn't give us much information to go on so it's hard to make a clear suggestion, but for my own KEGG data I'm quite happy using Cytoscape and also have recently been communicating networks using hive plots.

ADD COMMENTlink written 6.4 years ago by Josh Herr5.6k

Hi Josh. I also prefer the use of cytoscape, I'm just wondering about the best way to generate the input file for the specific task. I'll take a look at hive plots as well, thanks for the suggestion!

ADD REPLYlink written 6.4 years ago by Haji50
0
gravatar for balaji
5.9 years ago by
balaji40
Estonia
balaji40 wrote:

I have a followup question, I want to identify incoming and outgoing edges for eg. http://www.kegg.jp/kegg-bin/show_pathway?hsa00010 to Pentose phosphate pathway (PPP) edge 1 (outgoing) from PPP edge 3 (incoming) citrate cycle 1, 1 (out and incoming) proponate metabolism 1 (out) carbon fixation 1 (in) starch and sucrose 1,1 (in, out)

How can I extract this from .xml or from any file? I can access all kegg file.

ADD COMMENTlink written 5.9 years ago by balaji40
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