Visualization Of Biological Interactions (Sub-Pathways, Systems Biology Light)

Question

[Fredrik]

I'm looking for an easy and intuitive way to visualize subpathways of a receptor of interest. Basically, I have a target receptor and an end effect and I would like to be able to visualize the pathway between them. I would also like to be able to see other pathways affected to possibly find inhibitors that block certain effects from a "multiple-effect receptor". I suppose that it could be described as some sort of systems biology light approach where there's no need for quantitative data, nor time-dependence. Ideally, the solution should be easy enough to use that non-experts (in bioinformatics/systems biology that is) can use it to find interesting experiments to run in order to extend the knowledge around a certain pathway/receptor.

I have been looking some at the software list at http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix but the sheer mass of softwares listed makes the task of finding one fulfilling my needs a daunting task so if someone has a good suggestion, please leave it.

[added in edit] To further exemplify what I'm after, I would like to be able to construct schemes like Figure 1 in Swiech et. al., Role of mTOR in physiology and pathology of the nervous system, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2008, 116-132 ( http://dx.doi.org/10.1016/j.bbapap.2007.08.015 ). If possible, I'd gladly start with information found in different databases (such as Reactome, KEGG, BioModels etc.) and then extend it with data from literature.

Answer 1

[aidan-budd]

Tricky to know what to recommend without more information, but based on what you say here, you may find what you want here at STRING or STITCH, these would allow you/your collaborators to explore what's already known, and what is predicted (in some cases) about the interactions around your protein of interest. STITCH brings small molecules into the mix too, which might be useful if you're interested in looking for inhibitors?

Can also produce pretty visualisations of your interacitons?

Would be interesting to know if indeed this is useful for you in this context.

[Fredrik]

Thank you for your answer. It was not entirely what I was after, although the data in there most likely could help in finalizing the model. At the moment I'm more interested in software where I can assemble data from multiple sources, preferebly semi automated. I'll try to amend some more information to my question.