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A novel functional module detection algorithm for protein-protein interaction networks

A novel functional module detection algorithm for protein-protein interaction networks,10.1186/1748-7188-1-24,Algorithms for Molecular Biology,Woochan

A novel functional module detection algorithm for protein-protein interaction networks   (Citations: 23)
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BACKGROUND: The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM. RESULTS: STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced and graph topology. STM is found to be effective at detecting clusters with a diverse range of interaction structures that are significant on measures of biological relevance. The STM approach is compared to six competing approaches including the maximum clique, quasi-clique, minimum cut, betweeness cut and Markov Clustering (MCL) algorithms. The clusters obtained by each technique are compared for enrichment of biological function. STM generates larger clusters and the clusters identified have p-values that are approximately 125-fold better than the other methods on biological function. An important strength of STM is that the percentage of proteins that are discarded to create clusters is much lower than the other approaches. CONCLUSION: STM outperforms competing approaches and is capable of effectively detecting both densely and sparsely connected, biologically relevant functional modules with fewer discards.
Journal: Algorithms for Molecular Biology - Algorithms Mol Biol , vol. 1, no. 1, pp. 24-11, 2006
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    • ...Next, the comparison of HC-PIN and eight other clustering algorithms: MoNet [6], MCODE [19], DPClus [18], PINC [38], STM [39], MCL [40], [41], CMC [43], and Core-Attachment [44] is studied...
    • ...4.3 Comparison with Other Methods To evaluate the effectiveness of our algorithm HC-PIN, we compare it with several previous competing algorithms: MoNet [6], PINC [38], MCODE [19], DPClus [18], STM [39], MCL [40], [41], CMC [43] and Core-Attachment [44]...

    Jianxin Wanget al. A Fast Hierarchical Clustering Algorithm for Functional Modules Discov...

    • ...STM. Cho et al. [63] extended flow-based modularization approach called STM [64] to identify functional modules and protein complexes by considering the functional information...

    Xiaoli Liet al. Computational approaches for detecting protein complexes from protein ...

    • ...Recently, Hwang et al.[58] presented a novel functional module detection algorithm STM by using a pharmaco dynamic signal transduction network model...
    • ...STM consists of four steps [58]: (1) Compute signals transduced between all vertex pairs; (2) Select cluster representatives for each vertex; (3) Formation of preliminary clusters; (4) Merge preliminary clusters...

    Jianxin Wanget al. Recent advances in clustering methods for protein interaction networks

    • ...High-throughput assay methodologies, such as microarrays and mass spectrometry, have resulted in the rapid growth of protein data sets, the analysis of which can potentially yield insights into the mechanisms of human disease and the discovery of new therapeutic interventions[13]...
    • ...PPI data sets provide us the good opportunity to systematically analyze the structure of a large living system and also allow us to use it to understand essential principles like essentiality, genetic interactions, functions, functional modules, protein complexes and cellular pathways [13]...

    Lei Shiet al. Functional Flow Simulation Based Analysis of Protein Interaction Netwo...

    • ...High-throughput assay methodologies, such as microarrays and mass spectrometry, have resulted in the rapid growth of protein data sets, the analysis of which can potentially yield insights into the mechanisms of human diseases and the discovery of new therapeutic interventions [17][31]...

    Lei Shiet al. Semi-supervised learning protein complexes from protein interaction ne...

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