Question: Three network comparison using cytoscape
gravatar for ammasachu
8 days ago by
ammasachu0 wrote:


I have 100 highly interactive protein lists of three groups. and want to visualize in cytoscape. I wants to visualize the network with common genes in groups in different color. For example, Genes present in group A and B in one color , group A and C in another color and if present in all three in a different color. Ultimately I want a better and publication quality figure for the same.

Please let me know if need any more information Any advice in this regard will be really helpful.

Thanks in advance Aswathy

cytoscape network analysis • 121 views
ADD COMMENTlink modified 6 days ago • written 8 days ago by ammasachu0

Sorry for this.. i will add as comment/reply

ADD REPLYlink modified 5 days ago • written 6 days ago by ammasachu0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 6 days ago by genomax62k
gravatar for Jean-Karim Heriche
8 days ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

You can do it by assigning each node an attribute corresponding to each group or combination of groups and then apply a discrete mapping. Have a look at this post. For a more fancy representation in which a node would have more than one color if if belongs to more than one group, have a look at the enhancedGraphics app.

ADD COMMENTlink written 8 days ago by Jean-Karim Heriche18k

Thank you very much for the reply.

I have got another thought while trying this suggestion. The thing is , as I mentioned in above mail I want to visualize the 100 highly interactive proteins from three groups . I am writing the steps that I followed to get the network. Please let me know if I am doing right or is there any other way to do this.

I have a list of 100 GeneIDs as highly interactors and I imported in to cytoscape using Network from Public databases option. I have chosen STRING:Protein Query and pasted the identifiers after choosing arabidopsis thaliana as my species. That created a network for me based on my list, though it find little bit crowded to analyse!! Am I doing right?Is there any other way to get the network in more uncomplicated way?

Please give your input on the same.

Thank you. Aswathy

ADD REPLYlink written 5 days ago by ammasachu0

Yes there is another way, I suggest to read mcl clustering algorithm, you can create a distances matrix from blast and color them in cytoskape.

ADD REPLYlink written 5 days ago by Buffo1.2k
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