Gene network interconnectedness and the generalized topological overlap measure

Background: Network methods are increasingly used to represent the interactions of genes and/ or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. [1] can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could giv...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Andy M. Yip, Steve Horvath
• Keywords: BMCBI 2007, Proteins, Topological Overlap, Topological Overlap Measure