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Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method
Joint Authors
Zhou, Wei
Wang, Jianxin
Ren, Jun
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-30
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks.
Meanwhile, the large size of PPI network wants complex detection methods have low time complexity.
Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly.
In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values.
Then, it identifies protein complexes by expanding each seed to a λ-module.
MCSE is suitable for large PPI networks because of its low time complexity.
MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds.
MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th.
Experimental results of S.
cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database.
The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.
American Psychological Association (APA)
Ren, Jun& Zhou, Wei& Wang, Jianxin. 2014. Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method. BioMed Research International،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-502229
Modern Language Association (MLA)
Ren, Jun…[et al.]. Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method. BioMed Research International No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-502229
American Medical Association (AMA)
Ren, Jun& Zhou, Wei& Wang, Jianxin. Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-502229
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-502229