This vignette describes how to use data from an affinity purification-mass spectrometry experiment to generate relevant interaction networks, enriching the networks with information from public resources, analyzing the networks and creating effective visualizations. The result of this vignette will be a visualization of a human-HIV integrated network combining experimental data and publicly available interaction data.

In addition to importing networks in network file formats, such as sif and xgmml, Cytoscape also supports importing networks from tabular data. In this example, the data table represents protein-protein interaction data from a mass-spectrometry experiment.