Recently large scale experiments have provided new insights into the complex protein interaction network in yeast. However, previous analyses show that the number of interacting pairs that are common to different methods is extremely low and therefore less informative than expected. We show that comparing connectivities of individual proteins can reveal a common tendency between methods that has been missed by the pairwise comparison of interactions. We find significant correlations between experimental methods and also between various in silico methods. Exceptionally, a computational method, gene neighbourhood, correlates to both in silico and experimental approaches.

Hoffmann, R., Valencia, A. Protein interaction: Same network, different hubs. Trends Genet. 19(12), 681-683. (2003).

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