How to deal with very large and dense networks?

Too many nodes will make the network too dense to visualize and the computer slow to respond. We recommend limiting the total number of nodes to between 200 ~ 2000 for the best experience. We provide several Network Tools to help deal with network size when the networks are too large and complex to be visualized or interpreted. The basic idea is to focus only on those nodes that are more likely to be “important” as measured by their centrality within the network (see the previous FAQ for more details).

  1. Use Degree Filter to remove nodes with low degree centrality;
  2. Use Betweenness Filter to remove with low betweenness centrality;
  3. Use Shortest Path Filter to keep only the essential connectivity patterns of the network;
  4. Use Minimum Network or Steiner Forest Network to construct a minimally connected network that contains all of the seed genes
  5. Manually remove nodes or edges that are not of your interest from the Interaction Table page (most flexible)

The above approaches aim to reduce the network size and complexity and to retain the most relevant information for downstream functional analysis.