thank you very much. How to draw curve line in Cytoscape ?
On Thu, Apr 3, 2008 at 5:27 PM, ahmed essaghir <[EMAIL PROTECTED]> wrote: > 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 > -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: [EMAIL PROTECTED] eMail: [EMAIL PROTECTED] _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
