There are various structural measures like degree distribution, clustering coefficient, and many more. Apart from these basic topological, is there any other method or tool available which can precisely denote the driver nodes when we put a big omics data in this context ?
Hi, I‘m curious about what "driver nodes" you mentioned above acturally refers to? To my view, whatever kind of mathematical method was used to describe the topological feature of your built network, the final purpose for that is to understand the true biological meaning behind the complex system.
If you just want to investigate the dynamic features among network modules (or hubs), Cytoscape tool and BioGRID, Interact like databases will be a good choice. While if you are interested in dymaic and biological effects of those interections bewteen nodes combined with omics data (RNA-seq, ChIP-seq and etc.), pathway studio and biocyc will be useful, reference information of interactions will also be necessary.
Hope that helps!
Good luck!
Thanks Leavy Zhang.
I am more interested about studying controllability factor to understand the dynamicity of network. For instance, considering a case having two omics conditions: Healthy and Disease (along with expression values).
In my opinion, only using a single expression parameters doesn't solve the problem of deciphering the exact mechanism of action. So, I am looking for such method which be can be used with basic biological parameters to study driver nodes at different perturbations.
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