Importing Network From Table

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.

Background

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.

Import Network

  • Load the network via File → Import → Network from File...., and select the Example data.
  • In the Import Network from Table dialog, select the Bait column as Source Node and Prey column as Target Node.
  • Designate the AP-MS Score as an Edge Attribute.
  • Designate the HEKScore as a Target Node Attribute, by clicking in the column header and selecting the red spreadsheet icon.
  • Click OK to import the network.

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.

Import Network

The imported network consists of multiple smaller subnetworks, each representing a bait node and its associated prey nodes: