Analyzing Protein–Protein Interaction Networks

The advent of the “omics” era in biology
research
has brought new challenges and requires the development of novel strategies
to answer previously intractable questions. Molecular interaction
networks provide a framework to visualize cellular processes, but
their complexity often makes their interpretation an overwhelming
task. The inherently artificial nature of interaction detection methods
and the incompleteness of currently available interaction maps call
for a careful and well-informed utilization of this valuable data.
In this tutorial, we aim to give an overview of the key aspects that
any researcher needs to consider when working with molecular interaction
data sets and we outline an example for interactome analysis. Using
the molecular interaction database IntAct, the software platform Cytoscape,
and its plugins BiNGO and clusterMaker, and taking as a starting point
a list of proteins identified in a mass spectrometry-based proteomics
experiment, we show how to build, visualize, and analyze a protein–protein
interaction network.