Question: Is There A Web-Server Or Software That Can Create A Network Between Given Signaling Pathways?
0
gravatar for biosystat
6.1 years ago by
biosystat20
biosystat20 wrote:

Is there a web-server or software that can create a network between given signaling pathways? Imagine that we know about a number of pathways that are involved in a specific disease, now I would like to generate a network (topological net) between these pathways. In these networks, nodes are signaling pathways and edges indicates relationship between those pathways...

pathway enrichment network • 4.2k views
ADD COMMENTlink modified 5.2 years ago by emekdemir100 • written 6.1 years ago by biosystat20

How would you like to define the relationship between pathways? Within a given pathway the edges which connect nodes are typically defined by coexpression relationships between the corresponding genes, or known interactions between the proteins, or by known co-operation some biochemical reaction, etc. What will be your measure for the relatedness between pathways. Is iPath along the lines of what you are looking for?

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Obi Griffith17k

Please correct me if I am wrong here : Connection between nodes or relationship between pathways could be defined by subnetworks between any two pathways, for instance if you have two signaling pathways that proteins or genes of those two are connected ( it could be physical interaction or co-expression or even one protein that have same function in those two pathways) so they made a sub-networks, and we can consider them as a two nodes with at least one edge .

ADD REPLYlink written 6.1 years ago by biosystat20
1
gravatar for justinhaselbach
6.1 years ago by
United States
justinhaselbach250 wrote:

You may also try 'Reactome' Data sets [http://www.reactome.org/ReactomeGWT/entrypoint.html]. There is a Commercial One- Pathway Studio [http://www.ariadnegenomics.com/?id=41] from Ariadne Genomics, if you could try out. Thanks,

ADD COMMENTlink written 6.1 years ago by justinhaselbach250

Many thanks for your prompt answer, actually I am looking for a web-server of online software that could generate a topological network between my candidate signaling pathway, that indicates relationship between candidate pathways ...

ADD REPLYlink written 6.1 years ago by biosystat20
0
gravatar for Josh Herr
6.1 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

I'm unclear if you are looking for something specific or any general network analysis software. Um, I guess you haven't tried Cytoscape or are you looking for something different?

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Josh Herr5.6k

Hi Josh ,

Thank you very much for your suggestion, to be honest with you I have tried Cytoscape with colorful plugins! but still not satisfied, and now I am looking for a user-friendly web-server that can generate a weighted network between 5-10 signaling pathway! not within the signaling pathways

ADD REPLYlink written 6.1 years ago by biosystat20
0
gravatar for emekdemir
5.2 years ago by
emekdemir100
United States
emekdemir100 wrote:

Yes there is .. You can use PathwayCommons graph searches.

http://www.pathwaycommons.org/pc2/#graph

You can seed the paths-between search with the pathway members of 2 pathways. I'd suggest limiting yourself to a distance of 1 or 2 as chances are you will get a huge network back.

For more questions e-mail pc-info@pathwaycommons.org

I hope this helps, Emek

ADD COMMENTlink written 5.2 years ago by emekdemir100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1013 users visited in the last hour