Algorithms to Detect Multiprotein Modularity Conserved during Evolution
Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we present a linear-time algorithm, Produles, that improves on the running time of previous algorithms. We present a biologically motivated graph theoretic set of algorithm goals complementary to previous evaluation measures, demonstrate that Produles attains these goals more comprehensively than previous algorithms, and exhibit certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures.
Keywordsmodularity interactomes evolution algorithms
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- 9.Simon, H.A.: The structure of complexity in an evolving world: the role of near decomposability. In: Callebaut, W., Rasskin-Gutman, D. (eds.) Modularity: Understanding the Development and Evolution of Natural Complex Systems. Vienna Series in Theoretical Biology. MIT Press, Cambridge (2005)Google Scholar
- 10.Li, M., Wang, J., Chen, J., Pan, Y.: Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. In: Măndoiu, I., Narasimhan, G., Zhang, Y. (eds.) ISBRA 2009. LNCS (LNBI), vol. 5542, pp. 75–86. Springer, Heidelberg (2009)CrossRefGoogle Scholar
- 15.Hodgkinson, L., Karp, R.M.: Algorithms to detect multi-protein modularity conserved during evolution. EECS Department, University of California, Berkeley, Technical Report UCB/EECS-2011-7 (2011)Google Scholar
- 16.Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M., Sherlock, G.: Go:termfinder—open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20(18), 3710–3715 (2004)CrossRefGoogle Scholar