Gene Expression Network Analysis

Question

[shalinisonar]

Hi

I've constructed a network for oxidative stress pathway genes using bisogenet. I need to do network analysis.

I'm from a wet lab background & for the first time I'm using cytoscape, I've a few questions here..

1. I've seen many ppl generating random network, Is it necessary to construct random & compare it with our network?
2. I've a gene expression data of CVD in which i wanted to target specific pathway(oxidative stress). Can anyone suggest me work flow & plugin?
3. My 3rd question is do I have to use complete gene expression data or just the deferentially regulated (up or down) values as the node attributes?

So far my work flow is as follows

1. Construct oxidative stress network
2. Overlay gene expression data
3. Using Mcode identify highly clustered nodes & construct sub network
4. Sub-Network analysis
5. Identify Highly connected node
6. Go enrichment & Functional enrichment using DAVID

Can anyone suggest me am I going in a correct path? Any modification that u feel is necessary?

Thanks
Shalini

Answer 1

[Houkto]

I would also suggest using Biolayout for cluster analysis Link.

Answer 2

[Omid]

Following link might be useful. It works based on co-expression. Genenetwork/pathway and also to to have a network based on co-expression genenetwork/cytoscape