Dear list, Does anyone know of a method (tool), preferably available in BioC, that allows the drawing of an interaction network of which the topology is based on user-defined input? I have a set of (KEGG) pathways, of which i calculated an 'overlap index'. That is, the more genes are common in two sets the higher the overlap index score is. Now i would like to create a interaction network consisting of nodes (pathways) and edges such way that the overlap index determines the distance between the nodes (length of the edge). Thus, ideally, the higher the overlap index is between two pathways (nodes), the closer the nodes are grouped together in the network. I am new to this type of data representation and would appreciate any suggestion! Cytoscape? Currently i am visualizing this data using a heatmap but i think representation in an interaction network would be much more informative. Thanks, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]

On Thu, May 20, 2010 at 3:06 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Dear list, > > Does anyone know of a method (tool), preferably available in BioC, that > allows the drawing of an interaction network of which the topology is based > on user-defined input? > > I have a set of (KEGG) pathways, of which i calculated an 'overlap index'. > That is, the more genes are common in two sets the higher the overlap index > score is. > Now i would like to create a interaction network consisting of nodes > (pathways) and edges such way that the overlap index determines the distance > between the nodes (length of the edge). Thus, ideally, the higher the > overlap index is between two pathways (nodes), the closer the nodes are > grouped together in the network. > > Drawing networks is easy using the Rgraphviz package. See the 'graph' and 'Rgraphviz' vignettes. There's also a chapter on it in the Bioc case studies book. Michael I am new to this type of data representation and would appreciate any > suggestion! Cytoscape? Currently i am visualizing this data using a heatmap > but i think representation in an interaction network would be much more > informative. > > Thanks, > Guido > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> > email: guido.hooiveld@wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi, Guido I don't know other packages, but igraph (R package) can do similar stuff. It has tcl/tk interactive mode, but you can move the nodes to generate a goodlook netowrk. In other words, length of edge can be manually adjusted, however, you can use the width of edge for your index scores. The details can be found in the manual. Best Gilbert On 5/20/10 5:06 PM, "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> wrote: > Dear list, > > Does anyone know of a method (tool), preferably available in BioC, that allows > the drawing of an interaction network of which the topology is based on > user-defined input? > > I have a set of (KEGG) pathways, of which i calculated an 'overlap index'. > That is, the more genes are common in two sets the higher the overlap index > score is. > Now i would like to create a interaction network consisting of nodes > (pathways) and edges such way that the overlap index determines the distance > between the nodes (length of the edge). Thus, ideally, the higher the overlap > index is between two pathways (nodes), the closer the nodes are grouped > together in the network. > > I am new to this type of data representation and would appreciate any > suggestion! Cytoscape? Currently i am visualizing this data using a heatmap > but i think representation in an interaction network would be much more > informative. > > Thanks, > Guido > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Have a look at Gephi (http://gephi.org/) as an alternative to Cytoscape. They have a library to import graphs - python, php, c++ or java. Michael On 20/05/2010 6:06 PM, Hooiveld, Guido wrote: > Dear list, > > Does anyone know of a method (tool), preferably available in BioC, that allows the drawing of an interaction network of which the topology is based on user-defined input? > > I have a set of (KEGG) pathways, of which i calculated an 'overlap index'. That is, the more genes are common in two sets the higher the overlap index score is. > Now i would like to create a interaction network consisting of nodes (pathways) and edges such way that the overlap index determines the distance between the nodes (length of the edge). Thus, ideally, the higher the overlap index is between two pathways (nodes), the closer the nodes are grouped together in the network. > > I am new to this type of data representation and would appreciate any suggestion! Cytoscape? Currently i am visualizing this data using a heatmap but i think representation in an interaction network would be much more informative. > > Thanks, > Guido > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism& Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com<http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >