[BiO BB] How to make a network graphic using my genes in pathways?

Jinyan Huang 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:
> 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
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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: hiekeen at hotmail.com
eMail: hiekeen at gmail.com

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