Please use this identifier to cite or link to this item: https://doi.org/10.1186/1471-2105-10-169
Title: A core-attachment based method to detect protein complexes in PPI networks
Authors: Wu, M
Li, X 
Kwoh, C.-K
Ng, S.-K
Keywords: Biological studies
Comprehensive comparisons
Core-attachment structures
Dense region
Ppi networks
Protein complexes
Protein-protein interactions
State-of-the-art techniques
Proteins
Complex networks
algorithm
article
complex formation
computer prediction
controlled study
data mining
information processing
intermethod comparison
protein analysis
protein protein interaction
proteomics
Saccharomyces cerevisiae
chemistry
computer program
metabolism
methodology
protein analysis
protein database
protein domain
reproducibility
statistical analysis
multiprotein complex
protein
Algorithms
Data Interpretation, Statistical
Databases, Protein
Multiprotein Complexes
Protein Interaction Domains and Motifs
Protein Interaction Mapping
Proteins
Reproducibility of Results
Software
Issue Date: 2009
Citation: Wu, M, Li, X, Kwoh, C.-K, Ng, S.-K (2009). A core-attachment based method to detect protein complexes in PPI networks. BMC Bioinformatics 10 : 169. ScholarBank@NUS Repository. https://doi.org/10.1186/1471-2105-10-169
Rights: Attribution 4.0 International
Abstract: Background: How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes. Results: To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge. Conclusion: Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study. © 2009 Wu et al; licensee BioMed Central Ltd.
Source Title: BMC Bioinformatics
URI: https://scholarbank.nus.edu.sg/handle/10635/177953
ISSN: 14712105
DOI: 10.1186/1471-2105-10-169
Rights: Attribution 4.0 International
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