Difference between cross correlation value and node edge value

[Former user]

Hello sir, i am quite very new to this platform. i have just calculated the cross correlation matrix by LMI approach. the values lies between 0 to 1. for a particular case lets say C18=0.32. that means cross-correlation value between nod 1 and nod 8 is 0.32. now what i am thinking is that the network edge between nod 1 and nod 8 is also 0.32. Is that true? if not,

1. what is the difference between nod edge and cross-correlation value of a particular nod pair?
2. how bio3d calculates the network node edge?
3. is there any defaullt conditions for such nod edge calculations in bio3d?

regards

[Lars Skjærven]

Hi there,

That depends on your input for the cna function. Take note of the cutoff argument which defaults to 0.4. As the documentation says: Coupling below cutoff.cij are set to 0. Thus, if you use the default arguments, will be no edge between nodes 1 and 8. Similarly, a contact map can be provided to filter out edges (see argument cm). If you have multiple correlation matrices, e.g. from multiple simulations see function filter.dccm.

I would recommend consulting the general documentation of the cna() related functions in Bio3D (in the R console type help(cna) for more info on how the network is generated) as well as the CNA tutorial for more practical training (http://thegrantlab.org/bio3d/tutorials/protein-structure-networks). See also Yao et al (2016) (section Correlation Network Construction in the Methods section).

Hope this helps, L

[Xinqiu Yao]

Thanks for helping to answer, Lars! Just a quick reference, the input correlation values are converted to the -log() form by default in the 'cna()' function. That is, 0.32 will be converted to -log(0.32) for the edge, if the cutoff cutoff.cij is set to be below 0.32. As Lars suggested, going to read the help document, the tutorial, and our recent paper will be much more helpful.