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Figure 6 | BMC Systems Biology

Figure 6

From: Identifying disease-specific genes based on their topological significance in protein networks

Figure 6

Set of experimentally derived nodes K is colored red. We connect them by shortest path network S (blue nodes). The rest of the global network is represented by black nodes. In this example, the size of the global network N = 13, K = 7, and S = 5. The number of possible shortest path networks between node B and each of the other nodes in the global network which can contain D is 11 (N-2). The number of such networks which contain node D is 7 (N BD = 7). On the other hand, the number of shortest path networks containing D, among those connecting only nodes from the set K, is 5 (K BD = 5). The significance (p-value) for node D with respect to node B and set K can be calculated as p BD = p(N-2, N BD , K-1, K BD ). Similarly, we can calculate the other p-values for D with respect to A, G, K, J, I, and L, and then pick the smallest value and assign it as the significance of node D in the sub-network defined by the nodes of interest (red nodes). The nodes can be classified as internal (F, D, C, H, and M), source (A, B, and L) and target (A, G, K, J, and I) nodes.

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