STEP WISE ASSISTANCE TUTORIAL

DATA ANALYSIS: SECTION III: SIMULATION OF CLUSTERED PERTURBATIONS ON NETWORK

Pairs of genes or proteins often have parallel roles in the cellular milieu, and the effects of the removal of such coupled entities can affect the system negatively.Users can select any two nodes or edges from the network to simulate paired perturbations. In addition, the effect of perturbing larger clusters of nodes or edges from a network, rather than just pairs, can also be analyzed in this section of NEXCADE, by specifying upto nine vertices (or their edges).

The THIRD section of the Main Results Window shown below, allows users to carry out induced perturbation in pairs or clusters. [The format of this page is the same for both 'Your Web' and 'Browse Webs' sections of NEXCADE.]

On clicking manual 'Select Proteins' the following page is returned.

As shown above, five individual nodes have been selected by the program. Users can change each of these as desired, using the drop down menu for each node.
Alternatively, users can choose the most highly connected or least connected nodes in the network, and the program will select these automatically, as shown below:

In either selection mode, the following page will result after clicking 'Simulate' button for grouped perturbation:

As shown in the comparative table above, the five individual nodes when perturbed, lead to a loss of more than fifty nodes from the network, suggesting the occurence of multiple secondary extinctions. Users can view/save a list of the affected nodes by clicking the last link on this page.
Visualization of the reduced network can be done by clicking the second link. A list of the interactions in the remaining network can be viewed/saved by the third link and this list can be used as input to initiate the NEXCADE analysis and carry out further perturbations on this sub-network.

CLUSTERED EDGE PERTURBATION: As shown above, the first link allows users to select a certain number of edges or interactions to perturb in the given network.
For example, clicking on the 'Simulate' button after selecting three edges will result in the following:

As can be seen above, the five nodes selected earlier have a total of 68 interactions in the network. Users can select any three of these 68 using the drop down menu for each individual interaction.
Clicking the 'Remove' button after selecting three edges will result in simulation of edge perturbation and return the following:



The outcome of the perturbation analysis can be visualized as a comparative table depicting the changes in various network attributes as a response to the induced perturbation.