Assembling Global Maps of Cellular Function through Integrative Analysis of Physical and Genetic Networks

Rohith Srivas*, Gregory Hannum*, Johannes Rushcheinski, Keiichoro Ono, Peng-Liang Wang, Michael Smoot, Trey Ideker#

Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA 92093 USA

*These authors contributed equally to this work.
#To whom correspondence should be addressed:

     To take full advantage of large-scale genetic and physical interaction mapping projects, the enormous amount of raw data must first be assembled into models of cell structure and function. PanGIA (Physical and Genetic Interaction Alignment) is a plugin for the bioinformatics platform Cytoscape, 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. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 minutes and 30 minutes depending on the size of the dataset being analyzed.

PanGIA is a plugin for Cytoscape.
Download the PanGIA plugin (v1.1) here.

The protocol is not yet publicly available.

Supplementary data: