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

ahmed essaghir ahmed.essaghir at gmail.com
Thu Apr 3 05:27:07 EDT 2008

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

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