PanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies "modules" as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules.
In this latest version, PanGIA 3.0, the ability to completely control randomization was added with a new seed parameter. This will enable scientists to ensure completely reproducible results.
Tips for Use of PanGIA 3.0:
1. Always import physical and genetic networks into the same network collection before running PanGIA.
2. If importing networks from Excel, always name your sheets to the desired network name before importing. PanGIA sometimes has difficulty recognizing networks that are renamed later.
3. After importing physical and genetic networks and any annotations, save the session before running PanGIA. This will make it easier to experiment with input parameters. Usually, it is possible to run PanGIA repeatedly on the same physical and genetic networks without reloading the session. But you will most likely eventually want a "clean" session to work off of after discovering the best input parameters for your data.