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...
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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,
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 ...
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
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
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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?
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 .