Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/80062
Title: PLW : Probabilistic Local Walks for detecting protein complexes from protein interaction networks
Authors: Wong, Daniel Lin-Kit
Li, Xiaoli
Wu, Min
Zheng, Jie
Ng, See-Kiong
Keywords: DRNTU::Engineering::Computer science and engineering
Issue Date: 2013
Source: Wong, D. L., Li, X., Wu, M., Zheng, J., & Ng, S. (2013). PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. BMC genomics, 14(Suppl 5):S15.
Series/Report no.: BMC genomics
Abstract: Results: We designed a novel method called Probabilistic Local Walks (PLW) which clusters regions in a PPI network with high functional similarity to find protein complex cores with high precision and efficiency in O(|V| log |V| + |E|) time. A seed selection strategy, which prioritises seeds with dense neighbourhoods, was devised. We defined a topological measure, called common neighbour similarity, to estimate the functional similarity of two proteins given the number of their common neighbours.
Conclusions: Our proposed PLW algorithm achieved the highest F-measure (recall and precision) when compared to 11 state-of-the-art methods on yeast protein interaction data, with an improvement of 16.7% over the next highest score. Our experiments also demonstrated that our seed selection strategy is able to increase algorithm precision when applied to three previous protein complex mining techniques.
Background: Many biological processes are carried out by proteins interacting with each other in the form of protein complexes. However, large-scale detection of protein complexes has remained constrained by experimental limitations. As such, computational detection of protein complexes by applying clustering algorithms on the abundantly available protein-protein interaction (PPI) networks is an important alternative. However, many current algorithms have overlooked the importance of selecting seeds for expansion into clusters without excluding important proteins and including many noisy ones, while ensuring a high degree of functional homogeneity amongst the proteins detected for the complexes.
URI: https://hdl.handle.net/10356/80062
http://hdl.handle.net/10220/17886
ISSN: 1471-2164
DOI: 10.1186/1471-2164-14-S5-S15
Rights: © 2013 Wong et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
BioMed Central's Open Data policy. Unless otherwise stated, data included in published open access articles are distributed under the terms of the Creative Commons CC0 1.0 Public Domain Dedication waiver. This applies to data included in the article, its reference list(s) and its additional files.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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Wong_BMC-Genomics_2013_InCoB.pdfMain article1.72 MBAdobe PDFThumbnail
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wonglkd-PLW-7f8f0be - Binaries and sample data.zipBinaries and Sample Data832.4 kBUnknownView/Open
wonglkd-PLW-7f8f0be-Binaries and Sample Data.tar.gzBinaries and Sample Data831.98 kBUnknownView/Open
wonglkd-PLW-eb409f2-Predicted protein complexes.zipPredicted Protein Complexes451.35 kBUnknownView/Open
wonglkd-PLW-eb409f2-Predicted protein complexes.tar.gzPredicted Protein Complexes415.52 kBUnknownView/Open
wonglkd-PLW-5db2d50-PPI Datasets Used.zipPPI Datasets Used344.94 kBUnknownView/Open
wonglkd-PLW-5db2d50-PPI Datasets Used.tar.gzPPI Datasets Used344.57 kBUnknownView/Open
ppi.dip.cleaned-DIP.txtDIP(Database of Interacting Proteins)286.14 kBTextView/Open
ppi.combined6.cleaned-COMBINED6.txtCOMBINED6288.45 kBTextView/Open
Contact Us.txtAuthor's Contact107 BTextView/Open
README.md437 BUnknownView/Open
cmplx.3.newmips.tab-CYC2008 Catalogue.txtCYC2008 Catalogue37.9 kBTextView/Open
cmplx.3.cyc2008.tab-NewMIPS.txtNewMIPS13.93 kBTextView/Open
1471-2164-14-s5-s15-s1.pdfPerformance of Algorithms on Various Datasets537.79 kBAdobe PDFThumbnail
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