SMILE: A Novel Procedure for Subcellular Module Identification with Localization Expansion

We propose a novel procedure, Subcellular Module Identification with Localization 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 protein interaction networks in both the ComPPI and InWeb_InBioMap protein interaction datasets. Our results reveal that subcellular localization is a principal feature of functional modules and offers important guidance in detecting biologically meaningful results.

[1]  L. Tran,et al.  Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease , 2013, Cell.

[2]  Clara Pizzuti,et al.  Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods , 2014, Bioinform..

[3]  S. Brunak,et al.  A scored human protein–protein interaction network to catalyze genomic interpretation , 2017, Nature Methods.

[4]  Yijie Wang,et al.  Functional module identification in protein interaction networks by interaction patterns , 2014, Bioinform..

[5]  Xiaoli Li,et al.  Computational approaches for detecting protein complexes from protein interaction networks: a survey , 2010, BMC Genomics.

[6]  Stephen J Benkovic,et al.  Reversible Compartmentalization of de Novo Purine Biosynthetic Complexes in Living Cells , 2008, Science.

[7]  Haiyuan Yu,et al.  Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.

[8]  Dong Wang,et al.  CrossNorm: a novel normalization strategy for microarray data in cancers , 2016, Scientific Reports.

[9]  Tamás Korcsmáros,et al.  ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis , 2014, Nucleic Acids Res..

[10]  Erin K O'Shea,et al.  Signal-dependent dynamics of transcription factor translocation controls gene expression , 2011, Nature Structural &Molecular Biology.

[11]  Jason A. Papin,et al.  Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.