Comparing Subnetworks And Identifying Crucial Nodes In And Across Subnetworks

Question

[ChIP]

Hello Community!

I am at cross roads and confused regarding the approach to adopt, this is in reference to network building and comparison of networks.

I have three different networks made on the identical logic of drawing a edge between nodes if a gene is targeted by an miRNA

basically the input table is like

miRNA1  genex
miRNA2  geney
miRNA3  genex
...................

I used CytoHubba (plugin) to identify the subnetworks (feel free to suggest any better plugin).

I used small distance between the nodes as my filter (in case you are interested in knowing), and got three subnetworks for each of my input table.

So, three input tables and three subnetworks I have from this plugin.

My first question is: Is their any better tool/plugin which can identify and display subnetworks more efficiently?

Second question: how can I compare these three subnetworks and identify the unique and strong or driver nodes in each subnetworks and also common drivers of network.

Kindly help

Thank you

[Heather Vincent]

I am not sure that I understand what you are doing here. What are the differences in the datasets in the input tables? If you have 3 input tables, and 3 subnetworks from each input table, do you now have 9 subnetworks?

Answer 1

[ancient_learner]

For identifying "unique" nodes Advanced Network Merge can be used.try also Mcode (based on k-core algorithm), clusterone plugins for identifying the subnetworks.