Protopia: a protein-protein interaction tool

BackgroundProtein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data http://asp.uma.es.ResultsThe tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein.ConclusionThe tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks.

[1]  E. Golemis,et al.  Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system. , 2008, BioTechniques.

[2]  Werner Dubitzky,et al.  Fundamentals of Data Mining in Genomics and Proteomics , 2009 .

[3]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[4]  Javier De Las Rivas,et al.  Interactome Data and Databases: Different Types of Protein Interaction , 2004, Comparative and functional genomics.

[5]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[6]  Robin Palotai,et al.  Critical Review Chaperones as Integrators of Cellular Networks: Changes of Cellular Integrity in Stress and Diseases Structural Properties of Cellular Networks , 2007 .

[7]  Christina Kiel,et al.  Analyzing protein interaction networks using structural information. , 2008, Annual review of biochemistry.

[8]  Trey Ideker,et al.  Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species , 2008, Nucleic acids research.

[9]  Hanno Steen,et al.  Development of human protein reference database as an initial platform for approaching systems biology in humans. , 2003, Genome research.

[10]  T. Misteli.  The concept of self-organization in cellular architecture , 2001, The Journal of cell biology.

[11]  Qiong Gao,et al.  pSTIING: a ‘systems’ approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer , 2005, Nucleic Acids Res..

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

[13]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[14]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[15]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[16]  C. Rodríguez-Caso,et al.  The usefulness of post-genomics tools for characterization of the amine cross-talk in mammalian cells. , 2007, Biochemical Society transactions.

[17]  Amarnath Gupta,et al.  BiologicalNetworks: visualization and analysis tool for systems biology , 2006, Nucleic Acids Res..

[18]  Robert D. Finn,et al.  iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions , 2005, Bioinform..

[19]  Carlos Prieto,et al.  APID: Agile Protein Interaction DataAnalyzer , 2006, Nucleic Acids Res..

[20]  Luca Benini,et al.  TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders , 2008, Bioinform..

[21]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[22]  David James Sherman,et al.  ProViz: protein interaction visualization and exploration , 2005, Bioinform..

[23]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[24]  Kumaran Kandasamy,et al.  An evaluation of human protein-protein interaction data in the public domain , 2006, BMC Bioinformatics.

[25]  Ricard V Solé,et al.  Topology, tinkering and evolution of the human transcription factor network , 2005, The FEBS journal.

[26]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[27]  R. Solé,et al.  Networks in Cell Biology , 2007 .

[28]  D. Lane,et al.  The p53-Mdm2 pathway: targets for the development of new anticancer therapeutics. , 2003, Mini reviews in medicinal chemistry.

[29]  A. Valencia,et al.  A gene network for navigating the literature , 2004, Nature Genetics.

[30]  Robert E W Hancock,et al.  Complexities of targeting innate immunity to treat infection. , 2007, Trends in immunology.

[31]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[32]  R. Montañez,et al.  Information integration of protein-protein interactions as essential tools for immunomics. , 2006, Cellular immunology.

[33]  Bor-Sen Chen,et al.  A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining , 2008, BMC Medical Genomics.