I am looking for a tool, preferably online and freely available but it will tell you the proteins that would link 2 proteins that do not interact themselves. For example, the protein products of GRM5 and IL-6 do not interact but I imagine (although it may be very long) they will each interact with a variety of other proteins at which point you will find a common interaction. GRM5-Protein Z-Protein Y- Protein X - IL-6. Is there a tool available that might do this?
Thanks Kaue. I have used String before but it's not quite what I am looking for as it requires me to know what the intermediaries are whereas I am looking for something that will reveal them to me. Thank you though!
Sounds to me like you would like to know the path between two nodes (vertices). I graph theory the path describes the number of edges (lines) between two vertices. Don't have a direct answer, but you might search for graph theory path and software.
Hi Piers,
If you only have a relatively small number of proteins, GeneMANIA (http://genemania.org/) might help with this. Using your example, I put GRM5 and IL-6 in. It shows that PTPRE is in the same pathway as IL-6, PTPRE interacts with CALM1 and CALM1 interacts with GRM5.
Hope that helps
Maybe you can try ConsensusPathDB-human: http://cpdb.molgen.mpg.de/.
In the shortest interaction path, you can introduce the two proteins you want to connect. Then it shows the intermediate steps, along with information of the interaction such as pubmed id or a confidence score. In addition, it allows you to exclude a step in your path.
I hope that helps.
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