Question: Gene Expression Network Analysis
1
gravatar for shalinisonar
6.3 years ago by
shalinisonar10
Ernakulam
shalinisonar10 wrote:

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 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 Construct oxidative stress network Overlay gene expression data Using Mcode identify highly clustered nodes & construct sub network Sub-Network analysis Identify Highly connected node 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

gene expression • 3.2k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 6.3 years ago by shalinisonar10
1
gravatar for Houkto
6.3 years ago by
Houkto210
Houkto210 wrote:

I would also suggest using Biolayout for cluster analysis Link .

ADD COMMENTlink written 6.3 years ago by Houkto210
0
gravatar for Omid
6.3 years ago by
Omid540
Netherlands
Omid540 wrote:

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

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Omid540
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