Superclusteroid: a Web tool dedicated to data processing of protein-protein interaction networks

The study of proteins and the interactions between them, known as Protein-Protein Interactions (PPI), is extremely important in interpreting all biological cellular functions. In this article, a new web tool called Superclusteroid is presented which can analyse PPI data, in order to detect protein complexes or characterise the functionality of unknown proteins. The tool is essentially an intuitive PPI data processing pipeline. It supports various input file formats and provides services such as clustering, PPI network visualisation and protein cluster function prediction. Each Superclusteroid service can be used in a sequential manner or on an individual basis. In order to assess the reliability of our tool to infer PPIs, the results of the tool were compared to already known MIPS database complexes and a case scenario is presented where a known protein complex is predicted and the functionality of some of its proteins is revealed. Availability: Superclusteroid is freely available online at http://superclusteroid.uio.no/ .

[1]  J. Yates,et al.  TRAPP, a highly conserved novel complex on the cis‐Golgi that mediates vesicle docking and fusion , 1998, The EMBO journal.

[2]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[3]  Reinhard Schneider,et al.  jClust: a clustering and visualization toolbox , 2009, Bioinform..

[4]  Michele Magrane,et al.  UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.

[5]  Ron Shamir,et al.  A clustering algorithm based on graph connectivity , 2000, Inf. Process. Lett..

[6]  Emmanuel Pietriga,et al.  A toolkit for addressing HCI issues in visual language environments , 2005, 2005 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC'05).

[7]  Yves Deville,et al.  NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways , 2008, Nucleic Acids Res..

[8]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  W. Willats,et al.  Phage display: practicalities and prospects , 2002, Plant Molecular Biology.

[10]  Jacques van Helden,et al.  Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.

[11]  D. Bu,et al.  Topological structure analysis of the protein-protein interaction network in budding yeast. , 2003, Nucleic acids research.

[12]  H. Mewes,et al.  The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. , 2004, Nucleic acids research.

[13]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[14]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[15]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[16]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[17]  Igor Jurisica,et al.  Protein complex prediction via cost-based clustering , 2004, Bioinform..

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

[19]  Wojciech Szpankowski,et al.  Assessing Significance of Connectivity and Conservation in Protein Interaction Networks , 2006, RECOMB.

[20]  Rachael P. Huntley,et al.  The GOA database in 2009—an integrated Gene Ontology Annotation resource , 2008, Nucleic Acids Res..

[21]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[22]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[23]  Dieter Stoll,et al.  Protein microarrays: applications and future challenges. , 2005, Current opinion in drug discovery & development.

[24]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[25]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 2000, Nucleic Acids Res..