Finding a protein which have large interaction in a network

[Sasi]

Hi,
Iam Sasikala Rajendran doing project in protein protein interaction
network analysis.As Iam very new to this research area iam very
confused to select a protein in a network which has many number of
interacting partners.So please help me to solve this problem.My aim is
to select a protein having large number of ineracting partners i.e
that protein should have maximum interaction in that network....please
help me to solve this....I once again request you to help me.
Thanks in advance.

Thanking you
yours faithfully
R.SASIKALA

[Mike Smoot]

Hi,

I'm not sure I understand your question. Are you trying to find the most connected node in a network that you already have, or are you trying to create a network around one node that has many interactions?  If you've already got the network, then you should be able to use the Topology Filter in the Control Panel to find the most connected node.  You might also try the NetworkAnalyzer plugin available here: http://cytoscape.org/plugins/index.php.  If you need to create a network, then your best bet is to search databases like DIP, IntAct, PathwayCommons, or MiMI.  Once you've found a protein in one of those databases, you should be able to import the data into Cytoscape for further analysis.


Mike

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____________________________________________________________
Michael Smoot, Ph.D. Bioengineering Department
tel: 858-822-4756 University of California San Diego

[Maital Ashkenazi]

Hi Sasikala,

If you already have a network and you wish to find proteins with many
interactions, you can also do the following:
1) Layout --> Cytoscape Layouts --> Degree Sorted Circle Layout. This
action changes the network layout and adds a new attribute to each
node called Degree.
2) Display the Degree attribute in the data panel
3) Choose all the nodes in the network: Select --> Nodes --> Select
All Nodes (or use ctrl+A)
4) Click on the Degree column heading in the Node attribute browser to
sort the nodes list by the Degree attribute
5) The result is a sorted list of your proteins and the degree of
connectivity for each one.

Hope this helps,
Maital