Body: <p>I have a gene network that I clustered into 8 parts. I calculated the degree distribution of the clusters using Cytoscape and the slope of the clusters range from $0.7$ to about $1.3$.</p>
  
  <p>From literature <a href="https://en.wikipedia.org/wiki/Scale-free_network" rel="nofollow noreferrer">(reference)</a> usual scale free networks (real world networks) have a slope range of $2&gt;γ&gt;3$. What could be a reason for my network to have the smaller slope value?</p>
  
  <p>Edit: The number of nodes of each cluster ranges from 431 to 187 and the number of edges range from 1009 to 263. The network is bipartite in nature.  The clusters are all very sparse which can be understood by the number of edges in the largest and smallest cluster. Are real world biological networks not always scale free. Can anyone point me towards publications that mention this fact. I am just confused about why my network doesn't conform to the norm but maybe it doesn't need to. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-19T07:21:20.813Z
Comments.Text: Could you add more information about your network? How many nodes does it have? How are them distributed in your 8 clusters? What kind of data are you using to create it (It seems like gene expression, but I'm not sure) ?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-19T09:09:54.920Z
Comments.Text: Yes, please [edit] and explain more about your network. 8 clusters suggests your network is likely very small. Is it also sparse, as biological networks often are? You also seem to be starting with the assumption that your network is scale free. Is it? It might not be, after all.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-26T13:49:26.163Z
Comments.Text: @terdon Aren't real world biological networks scale free in nature? Or that's what I have been led to believe. I have not been able to find any publications to the contrary yet. What more information do you think I can provide about the network. I have mentioned the number of nodes and edges.
Comments.UserDisplayName: The Last Word
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-26T13:58:42.807Z
Comments.Text: Actual networks are [rarely scale free](https://arxiv.org/abs/1801.03400).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-26T14:26:50.080Z
Comments.Text: @Devon, this seems to be the answer rather a comment. Thanks for providing the reference (I lost it/I didn't save it when I read it). @ The Last Word: Despite not being a scale-free you can still work with your clusters, but take note that the topology of your network is not to be trusted.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-26T14:28:46.800Z
Comments.Text: @Llopis I'm hoping that someone else wants to give a more thorough answer than my link :)
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-26T14:51:17.120Z
Comments.Text: @Devon I think there was another paper about networks in biology, but in general it seems like people is using topologies analysis assuming too many things without (first) checking them.
Comments.UserDisplayName: llrs
Tags: <networks>
Title: The slopes of gene networks
ThreadText: # The slopes of gene networks
  
  (Asked by: username_0 on 2018-06-18)
  
  I have a gene network that I clustered into 8 parts. I calculated the degree distribution of the clusters using Cytoscape and the slope of the clusters range from $0.7$ to about $1.3$.
  
  From literature [(reference)](https://en.wikipedia.org/wiki/Scale-free_network) usual scale free networks (real world networks) have a slope range of $2>γ>3$. What could be a reason for my network to have the smaller slope value?
  
  Edit: The number of nodes of each cluster ranges from 431 to 187 and the number of edges range from 1009 to 263. The network is bipartite in nature. The clusters are all very sparse which can be understood by the number of edges in the largest and smallest cluster. Are real world biological networks not always scale free. Can anyone point me towards publications that mention this fact. I am just confused about why my network doesn't conform to the norm but maybe it doesn't need to.
  
  **Tags:** networks
  
  > **Comments:**
  > **username_1**: Could you add more information about your network? How many nodes does it have? How are them distributed in your 8 clusters? What kind of data are you using to create it (It seems like gene expression, but I'm not sure) ?  
  > **username_2**: Yes, please [edit] and explain more about your network. 8 clusters suggests your network is likely very small. Is it also sparse, as biological networks often are? You also seem to be starting with the assumption that your network is scale free. Is it? It might not be, after all.  
  > **username_0**: @username_2 Aren't real world biological networks scale free in nature? Or that's what I have been led to believe. I have not been able to find any publications to the contrary yet. What more information do you think I can provide about the network. I have mentioned the number of nodes and edges.  
  > **username_3**: Actual networks are [rarely scale free](https://arxiv.org/abs/1801.03400).  
  > **username_1**: @username_3, this seems to be the answer rather a comment. Thanks for providing the reference (I lost it/I didn't save it when I read it). @ username_0: Despite not being a scale-free you can still work with your clusters, but take note that the topology of your network is not to be trusted.  
  > **username_3**: @Llopis I'm hoping that someone else wants to give a more thorough answer than my link :)  
  > **username_1**: @username_3 I think there was another paper about networks in biology, but in general it seems like people is using topologies analysis assuming too many things without (first) checking them.  
  
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  ## 0 answers
  
  