hi! you can use Cytoscape www.cytoscape.org you can create your pathways graph by creating a .sif file (it's easy) a .sif file is a tab delimited one in which you have three columns : the first column contains the start nodes id and the second cotains an abreviation standing for the type of relationship between your nodes (pp for protein-protein, pr for protein-reaction, ...) and the third column contains the target nodes id : example : let's assume you havz a pathway like this in which a, b, c, d are proteins ids, so the relationship is "pp" a ----> b ----> c ---> d d---> b then your sif file will be like this a tabSpace b b tabSpace c c tabSpace d d tabSpace b
then you can open your graph using cytoscape and if you want to map you nodes (genes) in the graph you just do "select node from a file" (a file containing you genes of interest in the same ids of course as you used in the graph) then you'll have your genes hilighted where ever they are in the graph. also you can edit your graph in a user friendly way by deleting and adding arcs and nodes. you have also some plugins that allow you to highlight your genes according to their expression (if you have microarray data expression). have fun _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
