NDLI: RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks

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RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks

Content Provider	Springer Nature : BioMed Central
Author	Maruyama, Osamu Kuwahara, Yuki
Abstract	Background In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the problem of predicting protein complexes from a PPI network. This problem has two difficulties. One is related to small complexes, which contains two or three components. It is relatively difficult to identify them due to their simpler internal structure, but unfortunately complexes of such sizes are dominant in major protein complex databases, such as CYC2008. Another difficulty is how to model overlaps between predicted complexes, that is, how to evaluate different predicted complexes sharing common proteins because CYC2008 and other databases include such protein complexes. Thus, it is critical how to model overlaps between predicted complexes to identify them simultaneously. Results In this paper, we propose a sampling-based protein complex prediction method, RocSampler (Regularizing Overlapping Complexes), which exploits, as part of the whole scoring function, a regularization term for the overlaps of predicted complexes and that for the distribution of sizes of predicted complexes. We have implemented RocSampler in MATLAB and its executable file for Windows is available at the site, http://imi.kyushu-u.ac.jp/~om/software/RocSampler/ . Conclusions We have applied RocSampler to five yeast PPI networks and shown that it is superior to other existing methods. This implies that the design of scoring functions including regularization terms is an effective approach for protein complex prediction.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1920-5.pdf
Ending Page	62
Page Count	12
Starting Page	51
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-017-1920-5
Journal	BMC Bioinformatics
Issue Number	15
Volume Number	18
Language	English
Publisher	BioMed Central
Publisher Date	2017-12-06
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Protein-protein interaction Protein complex Markov chain Monte Carlo RocSampler Regularization term Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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