Additional file 1.

A Simple Illustration of How the Choice of a Similarity Measure Affects TOM. The TOM measure of interconnectedness is often used to define clusters of highly interconnected genes. Here we use very simple networks to highlight properties of the TOM measure. (a) Computing the topological overlap between genes 1 and 2 when all connection strengths between intermediate genes equal the constant a. (b) The numbers on the edges of the left network are correlations while the numbers on the edges of the networks on the right hand side equal corresponding unsigned adjacencies (upper network) and signed adjacencies (lower network). In a signed network, the topological overlap between genes 1 and 2 is very low because intermediate genes 3 and 4 have negative correlations with gene 1. In contrast, the topological overlap between genes 1 and 2 is high in an unsigned network.

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Mason et al. BMC Genomics 2009 10:327   doi:10.1186/1471-2164-10-327