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.
The data used for this protocol represents interactions between human and HIV proteins by Jäger et al. In this quantitative AP-MS experiment, a relatively small number of bait proteins were used to pull down a larger set of prey proteins.
Note: In cases where a Prey node interacts with more than one Bait node, it will have multiple rows of values for the same attribute (for example HEKScore). During import, the last value imported will overwrite prior values and visualizations using this attribute thus only shows the last value.
The imported network consists of multiple smaller subnetworks, each representing a bait node and its associated prey nodes: