Question: Fold change instead of expression (intensity values) in co-expression network?
gravatar for shalinisonar13
3.3 years ago by
shalinisonar1320 wrote:

Hi ,

can i use fold change instead of expression value for coexpression network construction analysis? We have performed global proteomic analysis between 3 condition (1)control 2) disease A and 3) disease B ). Objective is to check the differences in the PPI.

(Note: we have same set proteins between both the disease only difference is fold change)


Thank you


ADD COMMENTlink modified 3.3 years ago by Sam2.2k • written 3.3 years ago by shalinisonar1320
gravatar for maddy
3.3 years ago by
maddy20 wrote:

I don't think it's appropriate to use fold change for co-expression network construction. Simple reason is fold change's a pooled value and for correlation anything less then 3 samples would be a problem. Infact WGCNA requires minimum of 15 sample size. I would suggest you to use individual samples

ADD COMMENTlink written 3.3 years ago by maddy20

@maddy thank you for the quick response. We have performed the analysis on triplicates of two samples. Other issue is we have only control to case ratio values. Could you please suggest what else can be done??

ADD REPLYlink written 3.3 years ago by shalinisonar1320
gravatar for Sam
3.3 years ago by
Sam2.2k wrote:

With you sample size, it is rather unrealistic to build co-expression network and it might be better for you to find known networks that were enriched in your samples.

If you have the p-value of the difference, you can use the download a ppi information and look for enriched subnetworks using cytoscape. You can look into this but I am certain there is one function which helps you to reduce the network down to the significant subset and it is based on this paper: Discovering regulatory and signalling circuits in molecular interaction networks

, maybe you can try and find the function yourself as it was 2 years ago when I used it. 

ADD COMMENTlink written 3.3 years ago by Sam2.2k

@sam Thank you the article. 

ADD REPLYlink written 3.3 years ago by shalinisonar1320
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