The goal of network construction is to obtain a clear visualization of the biological context of the genes of interest. This includes capturing relevant biological pathways and molecules (TFs, drugs, chemicals) that interact with the gene list, as well as important connections between them.
- For a small gene list (< 100), this is accomplished by adding a substantial number of interacting nodes from the underlaying databases (i.e. first-order network).
- For a large gene list (> 1000), there are likely enough biological interactions within the uploaded list. Network construction is focused on finding potential relationships between those genes (i.e. zero-order network).
- For intermediate size (~100s), a common practice is to first create a first-order network, and then trim it using a variety of tools (i.e. Steiner Forest, minimum network, etc)