Hello Tim, On Thu, May 31, 2012 at 5:53 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > this seems clever, although I could swear that an existing package handles > graphical models of similar sorts. We could turn BioPAX/SBPAX into R graphs similar to the way rsbml does it. I wonder if there already are packages for using R graphs representing biological connections to model differential expression data? Then we may be able to use these. > but if the structural priors can be automatically pulled in (however that > might happen) and updated it would be cool as hell. Such data could be made available as SBPAX. BioPAX/SBPAX are excellent for merging data from multiple sources. Can you recommend any significant providers of such public data? Thanks! Take care Oliver > > > On Thu, May 31, 2012 at 2:47 PM, Oliver Ruebenacker <curoli at="" gmail.com=""> > wrote: >> >> ? ? Hello, >> >> ?I am exploring the idea of creating a package to import pathways as >> BioPAX/SBPAX (Level 3) data to analyze various measurements. In >> particular, differential microarray measurements could be used to >> identify upstream pathway nodes that seem to play a critical role in >> explaining the observed differences. >> >> ?The basic idea is very simple: consider a pathway that contains >> reactions A -> X, B -> X and B -> Y. If measurements show an increase >> in X, but not in Y, this would suggest an increase in A. If, however, >> we see increases of both X and Y, then this would point to an increase >> in B. Analogous considerations apply to nodes upstream of A and B. >> Negative correlations (by inhibition or depletion) will also be >> included. Consider this applied to a large network and a large set of >> measurements, which requires statistical tools to identify the most >> relevant upstream nodes. >> >> ?There are people using similar methods on similar data relying on >> quite simple evaluation functions and turning it into a profitable >> business. >> >> ?We can start with a simple prototype that can be created and >> deployed as quickly as possible as proof of concept to find interested >> parties. If there is sufficient interest, a more sophisticated version >> can be built. >> >> ?Different implementation approaches are possible. It seems to be >> simple and efficient to use rjava and have the reaction network >> extracted from BioPAX/SBPAX by a Java package that uses OpenRDF Sesame >> Rio (i.e. a small fraction of Sesame dealing with RDF graph >> representation and I/O). >> >> ?Any comment or show of interest is greatly appreciated. >> >> ?Thanks! >> >> ? ? Take care >> ? ? Oliver >> >> -- >> Oliver Ruebenacker >> Bioinformatics Consultant >> (http://www.knowomics.com/wiki/Oliver_Ruebenacker) >> Knowomics, The Bioinformatics Network (http://www.knowomics.com) >> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > A model is a lie that helps you see the truth. > > Howard Skipper > -- Oliver Ruebenacker Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker) Knowomics, The Bioinformatics Network (http://www.knowomics.com) SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)