Question: How To Get The Topology Of A Kegg Pathway?
0
gravatar for jlshi.nudt
5.6 years ago by
jlshi.nudt180
China
jlshi.nudt180 wrote:

Hi, all, is there a R package for get the topology of KEGG pathway? I get the gene list from GSEA gene sets, but how can I get the pathway topology, such as the node degree and egde attibution? Thank you.

pathway R • 3.0k views
ADD COMMENTlink modified 5.6 years ago by aheinzel110 • written 5.6 years ago by jlshi.nudt180

Short answer: get the data into a form that can be analysed using igraph.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Neilfws48k
2
gravatar for aheinzel
5.6 years ago by
aheinzel110
Austria
aheinzel110 wrote:

try using the R package KEGGgraph to get a graph object from KGML files (check the methods parseKGML, KEGGpathway2Graph and getKEGGedgeData). Subsequently, you could use (as already suggested before) igraph for further analysis.

ADD COMMENTlink written 5.6 years ago by aheinzel110
1
gravatar for Charles Warden
5.6 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

Not sure if there is an easy way to do this. Typically, KEGG enrichment is conducted the same way as GO enrichment (so, topology doesn't really matter).

That said, here are a couple suggestions:

1) KEGG pathways can be visualized here (somewhere there is also an option to upload fold-change values in order to color the pathway appropriately).

http://www.genome.jp/kegg/kegg2.html

2) There are some enrichment algorithms based upon topology (although I don't know for certain if they use KEGG)

http://genome.cshlp.org/content/17/10/1537

http://bioinformatics.oxfordjournals.org/content/25/1/75

I also developed the BD-Func algorithm to take positive versus negative regulation into consideration (although this is not based on the detailed graph characteristics):

https://peerj.com/articles/159/

ADD COMMENTlink written 5.6 years ago by Charles Warden7.2k

Thank you. I'll try these suggestions.

ADD REPLYlink written 5.6 years ago by jlshi.nudt180
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