 max planck institut
informatik # RINalyzer Tutorials

## Tutorials for Cytoscape 2.x

In the following, screenshots for each step appear when hovering the mouse over (image). If you cannot see the whole image, you can use the keyboard arrows to move to the right or to the bottom while holding the mouse over the image.

## Perform centrality analysis

• Go to AppsRINalyzerAnalyze Network (image ).
• In the RINalyzer Centrality Analysis dialog, you will see a warning (image ) informing you that the network contains more than one connected components. That is because the nodes A:40:_:GLY and B:37:_:SER are not connected to any other node in the network. You have two options:
• In the RINalyzer Centrality Analysis dialog, check the boxes of all centrality measures. You can get more information about each of the analysis settings by clicking the Help button at the bottom of the dialog or by visiting the Documentation page.
Here, we will show you four reasonable combinations.
1. Neglect weights and multiple edges: the centrality measures are computed assuming the edge weight between each pair of connected nodes is equal to one, i.e. choose the option Average weight. Setting the degree cutoff to 1 means that the degree of a node will be equal to the fraction of its first neighbors (image ).
2. Neglect weights and consider multiple edges: the centrality measures are computed assuming the edge weight between each pair of connected nodes is equal to the number of edges between the two nodes. Since the edge weights will be proportional to the number of edges, we need to choose a method to convert them into distances. We can set the degree cutoff to 3, i.e., the degree will be equal to the fraction of nodes that are connected by at most 3 edges to the node of interest (image ).
3. Consider weights and multiple edges: choose the edge attribute NrInteractions (an integer value representing the number of interactions between two residues) and the option Sum of weights. Then, the centrality measures are computed assuming that the edge weight between each pair of connected nodes is equal to the sum of the weights of all edges connecting the two nodes. We choose the max-value method for converting scores into distances. In this case, the degree (with cutoff set to 5) will be equal to the fraction of nodes that are at most at distance 5 from the node of interest (image ).
4. Consider weights and only one edge type: choose the edge attribute InteractionScore and the edge type combi:all_all, which represents the overall residue interactions, i.e., the centrality measures will be computed assuming the edge weight between each pair of nodes is equal to the weight of the cobmi:all_all edge connecting them. We can set the method for converting scores into distances to max-value and the degree cutoff to 2 (image ).
• After setting the appropriate values for each setting, click the Analyze button.
• A Progress... dialog showing the progress of the analysis will appear (image ). The time for computing the centrality measures depends on the size of the network and the number of selected nodes. You can cancel the analysis any time by clicking the Cancel button in the Progress... dialog.
• After a successful computation, you can see the results in the RINalyzer Centralities tab of the Cytoscape's Results Panel (image ).