Abstract
Substantial progress has been made in the field of “omics” research (e.g., Genomics, Transcriptomics, Proteomics, and Metabolomics), leading to a vast amount of biological data. In order to represent large biological data sets in an easily interpretable manner, this information is frequently visualized as graphs, i.e., a set of nodes and edges. Nodes are representations of biological molecules and edges connect the nodes depicting some kind of relationship.
Obviously, there is a high demand for computer-based assistance for both visualization and analysis of biological data, which are often heterogeneous and retrieved from different sources. This chapter focuses on software tools that assist in visual exploration and analysis of biological networks. Global requirements for such programs are discussed. Utilization of visualization software is exemplified using the widely used Cytoscape tool. Additional information about the use of Cytoscape is provided in the Notes section. Furthermore, special features of alternative software tools are highlighted in order to assist researchers in the choice of an adequate program for their specific requirements.
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References
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R et al (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261
Ashburner M, Ball CA, Blake JA, Butler H, Cherry JM, Corradi J et al (2001) Creating the gene ontology resource: design and implementation. Genome Res 11:1425–1433
Vailaya A, Bluvas P, Kincaid R, Kuchinsky A, Creech M, Adler A (2005) An architecture for biological information extraction and representation. Bioinformatics 21:430–438
Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform 4:2
Maere S, Heymans K, Kuiper M (2005) BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C et al (2007) Integration of biological networks and gene expression data using cytoscape. Nat Protoc 2:2366–2382
Rho S, You S, Kim Y, Hwang D (2008) From proteomics toward systems biology: integration of different types of proteomics data into network models. BMB Rep 41:184–193
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–34
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M et al (2005) STRING: known and predicted protein–protein associations, integrated and transferred across organisms. Nucleic Acids Res 33:D433–D437
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J et al (2009) STRING 8: a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37:D412–D416
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD (2005) Querying and computing with BioCyc databases. Bioinformatics 21:3454–3455
Shannon PT, Reiss DJ, Bonneau R, Baliga NS (2006) The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinform 7:176
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N et al (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34:374–378
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80
Team RDC (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
Bare JC, Shannon PT, Schmid AK, Baliga NS (2007) The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinform 8:456
Klukas C, Junker BH, Schreiber F (2006) The VANTED software system for transcriptomics, proteomics and metabolomics analysis. J Pestic Sci 31:289–292
Junker BH, Klukas C, Schreiber F (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinform 7:109
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 96:1254–1265
Funahashi A, Tanimura N, Morohashi M, Kitano H (2003) Cell Designer: a process diagram editor for gene-regulatory and biochemical networks. BioSilico 1:159–162
Kitano H, Funahashi A, Matsuoka Y, Oda K (2005) Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 23:961–966
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531
Hucka M, Finney A, Sauro H, Kovitz B, Keating S, Matthews J et al. (2003) Introduction to the systems biology workbench. [http://www.sys-bio.org/caltechSBW/sbwDocs/docs/index.html]
Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J et al (2003) Next generation simulation tools: the systems biology workbench and BioSPICE integration. OMICS 7:355–372
Ulitsky I, Gat-Viks I, Shamir R (2008) MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biol 9:R1
Iragne F, Nikolski M, Mathieu B, Auber D, Sherman D (2005) ProViz: protein interaction visualization and exploration. Bioinformatics 21:272–274
Baitaluk M, Sedova M, Ray A, Gupta A (2006) Biological networks: visualization and analysis tool for systems biology. Nucleic Acids Res 34:W466–W471
Baitaluk M, Qian XF, Godbole S, Raval A, Ray A, Gupta A (2006) PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinform 7:55
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N et al (2005) Towards a proteome-scale map of the human protein–protein interaction network. Nature 437:1173–1178
Agne B, Meindl NM, Niederhoff K, Einwachter H, Rehling P, Sickmann A et al (2003) Pex8p: an intraperoxisomal organizer of the peroxisomal import machinery. Mol Cell 11:635–646
Acknowledgments
This work is funded by the Bundesministerium für Bildung und Forschung (BMBF, grant 01 GS 08143) and by the Deutsche Forschungsgemeinschaft within the SFB 642. Thanks are also due to the Agilent Laboratories and Annette Adler for the financial support for the color versions of the figures.
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Kohl, M., Wiese, S., Warscheid, B. (2011). Cytoscape: Software for Visualization and Analysis of Biological Networks. In: Hamacher, M., Eisenacher, M., Stephan, C. (eds) Data Mining in Proteomics. Methods in Molecular Biology, vol 696. Humana Press. https://doi.org/10.1007/978-1-60761-987-1_18
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DOI: https://doi.org/10.1007/978-1-60761-987-1_18
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