How To Get The Topology Of A Kegg Pathway?
2
0
Entering edit mode
10.9 years ago
jlshi.nudt ▴ 240

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 • 5.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
10.9 years ago
aheinzel ▴ 130

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 COMMENT
1
Entering edit mode
10.9 years ago

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 COMMENT
0
Entering edit mode

Thank you. I'll try these suggestions.

ADD REPLY

Login before adding your answer.

Traffic: 1084 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6