Question: What if a network is not scale-free?
0
gravatar for Arindam Ghosh
9 months ago by
Arindam Ghosh160
India
Arindam Ghosh160 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 • 565 views
ADD COMMENTlink written 9 months ago by Arindam Ghosh160
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 9 months ago • written 9 months ago by Devon Ryan89k

Can you suggest some paper regarding this?

ADD REPLYlink written 9 months ago by Arindam Ghosh160

sure

ADD REPLYlink written 9 months ago by Devon Ryan89k

@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 9 months ago by krushnach80480
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 9 months ago by Devon Ryan89k

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 9 months ago by krushnach80480

Yeah, just take it as it is.

ADD REPLYlink written 9 months ago by Devon Ryan89k
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