Three network comparison using cytoscape

Question

[ammasachu]

Hi,

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

[ammasachu]

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

[GenoMax]

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

Answer 1

[Jean-Karim Heriche]

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.

[ammasachu]

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

[Buffo]

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.