SMILE: a novel procedure for subcellular module identification with localisation expansion
- Author(s): Lixin Cheng 1 ; Pengfei Liu 1 ; Kwong-Sak Leung 1
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View affiliations
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Affiliations:
1:
Department of Computer Science & Engineering , Chinese University of Hong Kong , Ma Liu Shui , Hong Kong
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Affiliations:
1:
Department of Computer Science & Engineering , Chinese University of Hong Kong , Ma Liu Shui , Hong Kong
- Source:
Volume 12, Issue 2,
April
2018,
p.
55 – 61
DOI: 10.1049/iet-syb.2017.0085 , Print ISSN 1751-8849, Online ISSN 1751-8857
Computational clustering methods help identify functional modules in protein–protein interaction (PPI) network, in which proteins participate in the same biological pathways or specific functions. Subcellular localisation is crucial for proteins to implement biological functions and each compartment accommodates specific portions of the protein interaction structure. However, the importance of protein subcellular localisation is often neglected in the studies of module identification. In this study, the authors propose a novel procedure, subcellular module identification with localisation expansion (SMILE), to identify super modules that consist of several subcellular modules performing specific biological functions among cell compartments. These super modules identified by SMILE are more functionally diverse and have been verified to be more associated with known protein complexes and biological pathways compared with the modules identified from the global PPI networks in both the compartmentalised PPI and InWeb_InBioMap datasets. The authors’ results reveal that subcellular localisation is a principal feature of functional modules and offers important guidance in detecting biologically meaningful results.
Inspec keywords: proteins; cellular biophysics; molecular biophysics
Other keywords: computational clustering methods; protein subcellular localisation; subcellular modules; protein-protein interaction network; localisation expansion; subcellular module identification; subcellular localisation; biological functions; protein interaction structure; InWeb-InBioMap datasets
Subjects: Biomolecular interactions, charge transfer complexes; Cellular biophysics
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