How to assign manually biological function into nodes in Cytoscape?

Question

[Omid]

I have a network created by cytoscape including 354 genes(nodes) and the genes have connected by different edges(pathway, PPI, genetic interaction, domain and co-localization).

I have manually grouped these 354 genes in 10 groups based on their biological functions.

Now I want to assign these biological function for each gene. There are some genes which are involving in more than one function. The question is how I can prepare a new network by cytoscape in which shows these biological functions . Please consider I am not bioinformatician;) so please show me the easy way if possible. Thanks in advance.

Answer 1

[Nicolas Rosewick]

One idea to draw such graph is to define a bipartite network where each gene is assigned to one ore more function like this in a tab delimited file:

geneA    function1
geneA    function2
geneA    function3
geneB    function2
geneB    function4

After that you load this file into cytoscape. And you can apply the bipartite layout. Or organic layout. And also you can maybe define the node size by degree of connection

[Omid]

Thanks NicoBxl,

You mean I add a new column in table panel section and then write functions?

I checked it it dose not answer

[Nicolas Rosewick]

No create a new document containing for each line an association gene-function . Per example, If a gene is involved in multiple function (say 6 functions), you will have 6 lines for this gene like :

gene    function1
gene    function2
gene    function3
gene    function4
gene    function5
gene    function6

After that, import this file into cytoscape

[Omid]

Thanks a lot it works and if I want to show the other edges like pathway a PPI , ... how can I show them?