What if the input gene list is very large (> 1000)?

When there are a large number of significant genes or seed proteins, the resulting networks will be too large and complex for effective visualization and interpretation. NetworkAnalyst offers four possible solutions:

  1. Build the network using Zero-order option in the network building dialog instead of default first-order; (Only applicable to PPI network)
  2. Trim the networks to keep only seeds and their connecting nodes using Minimum Network or Steiner Forest Network;
  3. Filter the networks using the Degree Filter or Betweenness Filter;
  4. Reduce the input genes by using larger fold change and/or smaller p value cutoffs.

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