The Cytoscape App counts triplets and computes z-scores against randomly generated networks. In addition, it plots significance profiles and lists motifs for each node in the network reporting in a separate column the functional class the protein (node) belongs to (Transcription factor, receptor, phosphatase, kinase) which can be used in further statistical and machine learning studies.
The user has to create a “Network View” and start the App from the dedicated Cytoscape menu option.
A pop-up configuration window asks the user to specify the edge attribute used to discriminate the two interaction signs (classes) to analyze (Activation/Inhibition). Other than this, the application can randomly generate networks similar to the one defined by the user and calculate motifs z-scores and significance profiles.
When the analysis is completed the Cytoscape App shows a floating window which reports results already partially analyzed.
The floating window contains 5 main tabs.
1. Closed Triplets which reports the relative abundance of each closed triangle in the network.
2. Linear Triplets which reports the relative abundance of linear triplets in the network.
3. Significance Profile reports the profile of the network analyzed as a line chart.
4. Data reports for each motif its abundance in the analyzed network and in randomly generated ones together with standard deviation, z-scores and significance profile score.
5. Motifs Table contains the entire list of motifs for each node in the network for further analysis and possibly machine learning classification approaches.
A toy project can be downloaded here:
A project with real signaling networks can be downloaded here:
Alberto Calderone - email@example.com