[BiO BB] How to make a network graphic using my genes in pathways?
hiekeen at gmail.com
Wed Apr 16 23:54:27 EDT 2008
thank you very much.
How to draw curve line in Cytoscape ?
On Thu, Apr 3, 2008 at 5:27 PM, ahmed essaghir <ahmed.essaghir at gmail.com> wrote:
> 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
> 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
> BBB at bioinformatics.org
Jinyan Huang (ekeen)
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