A survey of visualization tools for biological network analysis

The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing.

[1]  Andre Skusa,et al.  Extraction of biological interaction networks from scientific literature , 2005, Briefings Bioinform..

[2]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[3]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[4]  Ivan Bratko,et al.  GenePath: a system for automated construction of genetic networks from mutant data , 2003, Bioinform..

[5]  J I Kim,et al.  Personal networks and the adoption of family planning in rural Korea. , 1984, In'gu pogon nonjip = Journal of population and health studies.

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

[7]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[8]  Christian von Mering,et al.  STITCH: interaction networks of chemicals and proteins , 2007, Nucleic Acids Res..

[9]  Andreas Ludwig,et al.  A Fast Adaptive Layout Algorithm for Undirected Graphs , 1994, GD.

[10]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[11]  Matthew Suderman,et al.  Tools for visually exploring biological networks , 2007, Bioinform..

[12]  M. Tyers,et al.  Osprey: a network visualization system , 2003, Genome Biology.

[13]  Ron Shamir,et al.  PIVOT: Protein Interacions VisualizatiOn Tool , 2004, Bioinform..

[14]  Patrick Lambrix,et al.  Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX , 2005, Bioinform..

[15]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[16]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[17]  Hubert Hackl,et al.  Java editor for biological pathways , 2003, Bioinform..

[18]  A Finney,et al.  Systems biology markup language: Level 2 and beyond. , 2003, Biochemical Society transactions.

[19]  Emek Demir,et al.  PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways , 2002, Bioinform..

[20]  Akihiko Konagaya,et al.  KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data , 2003, Bioinform..

[21]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the World Wide Web. 4. CML Schema , 2003, J. Chem. Inf. Comput. Sci..

[22]  E. Minch,et al.  pathSCOUTTM: exploration and analysis of biochemical pathways , 2003, Bioinform..

[23]  A. Brazma,et al.  Standards for systems biology , 2006, Nature Reviews Genetics.

[24]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[25]  Gary D. Bader,et al.  BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation , 2005 .

[26]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[27]  Peer Bork,et al.  Medusa: a simple tool for interaction graph analysis , 2005, Bioinform..

[28]  Christopher J. Rawlings,et al.  Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures , 2004, Silico Biol..

[29]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[30]  Holger Karas,et al.  TRANSFAC: a database on transcription factors and their DNA binding sites , 1996, Nucleic Acids Res..

[31]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[32]  Matthias Zwicker,et al.  Ieee Transactions on Visualization and Computer Graphics Ewa Splatting , 2002 .

[33]  Maurizio Lenzerini,et al.  Data integration: a theoretical perspective , 2002, PODS.

[34]  Leslie D. Ball,et al.  DRASTIC—INSIGHTS: querying information in a plant gene expression database , 2005, Nucleic Acids Res..

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

[36]  Dan Brickley,et al.  Rdf vocabulary description language 1.0 : Rdf schema , 2004 .

[37]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , 1999, J. Chem. Inf. Comput. Sci..

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

[39]  Edgar Wingender,et al.  TRANSPATH: An integrated database on signal transduction and a tool for array analysis , 2003, Nucleic Acids Res..

[40]  Akihiko Konagaya,et al.  GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs , 2003, Bioinform..

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

[42]  Roberto Therón,et al.  BicOverlapper: A tool for bicluster visualization , 2008, Bioinform..

[43]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[44]  S. Rhee,et al.  MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.

[45]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information , 2021, Nucleic Acids Res..

[46]  Stuart L. Schreiber,et al.  SpectralNET – an application for spectral graph analysis and visualization , 2005, BMC Bioinformatics.

[47]  Christopher J. Rawlings,et al.  Graph-based analysis and visualization of experimental results with ONDEX , 2006, Bioinform..

[48]  David R. Gilbert,et al.  MetaNetter: inference and visualization of high-resolution metabolomic networks , 2008, Bioinform..

[49]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[50]  Peter D. Karp,et al.  The Pathway Tools software , 2002, ISMB.

[51]  Dan Brickley,et al.  Resource Description Framework (RDF) Model and Syntax Specification , 2002 .

[52]  Angeline M. Loh,et al.  Celestial3D: a novel method for 3D visualization of familial data , 2008, Bioinform..

[53]  Stijn van Dongen,et al.  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data , 2007, PLoS Comput. Biol..

[54]  Imre Vastrik,et al.  Reactome: a knowledgebase of biological pathways , 2004, OTM Workshops.

[55]  S. R. Hiltz,et al.  The International Network for Social Network Analysis , 1984 .

[56]  Richard Bruskiewich Meeting Review: Plant Bioinformatics at the NSF and NPGI (PAMGX Satellite) Meetings , 2002, Comparative and functional genomics.

[57]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[58]  M. Sheelagh T. Carpendale,et al.  VisLink: Revealing Relationships Amongst Visualizations , 2007, IEEE Transactions on Visualization and Computer Graphics.

[59]  Kaveh G Shojania,et al.  Searching the health care literature efficiently: from clinical decision-making to continuing education. , 2002, American journal of infection control.

[60]  Allan R. Wilks,et al.  Visualizing Network Data , 1995, IEEE Trans. Vis. Comput. Graph..

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

[62]  Falk Schreiber,et al.  VANTED: A system for advanced data analysis and visualization in the context of biological networks , 2006, BMC Bioinformatics.

[63]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[64]  Alexander E. Kel,et al.  TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations , 2005, Nucleic Acids Res..

[65]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

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

[67]  Nizar N Batada,et al.  CNplot: visualizing pre-clustered networks. , 2004, Bioinformatics.

[68]  Andrei N. Lupas,et al.  CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..

[69]  David Auber,et al.  Tulip - A Huge Graph Visualization Framework , 2004, Graph Drawing Software.

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

[71]  The Plant Ontology Consortium The Plant Ontology™ Consortium and Plant Ontologies , 2002, Comparative and functional genomics.

[72]  John W. Pinney,et al.  metaSHARK: a WWW platform for interactive exploration of metabolic networks , 2006, Nucleic Acids Res..

[73]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[74]  Peter Murray-Rust,et al.  Development of chemical markup language (CML) as a system for handling complex chemical content , 2001 .

[75]  Vladimir Batagelj,et al.  Pajek - Program for Large Network Analysis , 1999 .

[76]  kc claffy,et al.  Otter: A general-purpose network visualization tool , 1999 .