Question: What if a network is not scale-free?
0
gravatar for Arindam Ghosh
14 months ago by
Arindam Ghosh170
India
Arindam Ghosh170 wrote:

I have built a gene coexpression data from RNAseq data sets using the protocol as mentioned in the paper Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. I wanted to check if my network is scale-free as most biological networks are. Using cytoscape network analyser I got the node degree distribution and on fitting the power law, the value of gamma is 0.5. For scale free network it usually between 2 and 3. Neither does it have a bell shaped curve to be random network. How do I interpret this?

rna-seq cytoscape network • 771 views
ADD COMMENTlink written 14 months ago by Arindam Ghosh170
1

Most biological networks are NOT scale free, the earlier hype about that was wrong. It would also be VERY surprising if a biological network were actually random.

ADD REPLYlink modified 14 months ago • written 14 months ago by Devon Ryan91k

Can you suggest some paper regarding this?

ADD REPLYlink written 14 months ago by Arindam Ghosh170

sure

ADD REPLYlink written 14 months ago by Devon Ryan91k

@Devon I saw the paper ,"Most biological networks are NOT scale free" so now the question ,i have used WGCNA most of the time i go for scale free network ,so that is not true going by the paper you cited ?

ADD REPLYlink written 14 months ago by krushnach80580
1

Correct, as the paper says, most networks are not scale free. Even the ones in the WGCNA documentation aren't (at least from a cursory look). Optimize of the highest soft power and leave it at that.

ADD REPLYlink written 14 months ago by Devon Ryan91k

to extend my curiosity what ever WGCNA paper or paper that used WGCNA for analysis mentioned as scale free network ,so whatever result they have given so far would that be taken as it is ?

ADD REPLYlink written 14 months ago by krushnach80580

Yeah, just take it as it is.

ADD REPLYlink written 14 months ago by Devon Ryan91k
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