Abstract
Visualization is a powerful method to present and explore a large amount of data. It is increasingly important in the life sciences and is used for analyzing different types of biological data, such as structural information, high-throughput data, and biochemical networks. This chapter gives a brief introduction to visualization methods for bioinformatics, presents two commonly used techniques in detail, and discusses a graphical standard for biological networks and cellular processes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Tsai CS (2003) Molecular graphics: visualization of biomolecules. In: Introduction to computational biochemistry. John Wiley & Sons, Inc., pp 53–71
Can T, Wang Y, Wang YF, Su J (2003) FPV: fast protein visualization using Java3D. Bioinformatics 19(8):913–922
Stivala A, Wybrow M, Wirth A, Whisstock JC, Stuckey PJ (2011) Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics 27(23):3315–3316
Helt GA, Lewis S, Loraine AE, Rubin GM (1998) BioViews: Java-based tools for genomic data visualization. Genome Res 8(3):291–305
Kerkhoven R, van Enckevort FHJ, Boekhorst J, Molenaar D, Siezen RJ (2004) Visualization for genomics: the microbial genome viewer. Bioinformatics 20(11):1812–1814
Naquin D, d’Aubenton-Carafa Y, Thermes C, Silvain M (2014) CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data. BMC Bioinformatics 15:198
Andrews DF (1972) Plots of high-dimensional data. Biometrics 29:125–136
Inselberg A, Dimsdale B (1990) Parallel coordinates: a tool for visualizing multi-dimensional geometry. In: Proc. Visualization, pp 361–370
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868
Baehrecke EH, Dang N, Babaria K, Shneiderman B (2004) Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5(1):84
Hughes T, Hyun Y, Liberles D (2004) Visualising very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinformatics 5(1):48
Rost U, Bornberg-Bauer E (2002) TreeWiz: interactive exploration of huge trees. Bioinformatics 18(1):109–114
Huson D, Richter D, Rausch C, Dezulian T, Franz M, Rupp R (2007) Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8(1):460
Schreiber F (2002) High quality visualization of biochemical pathways in BioPath. In Silico Biol 2(2):59–73
Sirava M, Schäfer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E, Lenhof HP (2002) BioMiner—modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 18(suppl 2):S219–S230
Kerren A, Schreiber F (2014) Network visualization for integrative bioinformatics. In: Hofestädt R, Chen M (eds) Approaches in Integrative Bioinformatics: towards the virtual cell. Springer, New York, pp 173–202
Molw PDB Viewer 4.0
Junker BH, Klukas C, Schreiber F (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7:109
Forster M, Pick A, Raitner M, Schreiber F, Brandenburg FJ (2002) The system architecture of the BioPath system. In Silico Biol 2(3):415–426
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA et al (2010) Visualization of omics data for systems biology. Nat Methods 7:S56–S68
Duggan D, Bittner B, Chen Y, Meltzer P, Trent J (1999) Expression profiling using cDNA microarrays. Nat Genet 21(Suppl 1):11–19
MacBeath G (2002) Protein microarrays and proteomics. Nat Genet 32(Suppl 1):526–532
Villas-Boas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24(5):613–646
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98:4569–4574
Genc B, Dogrusöz U (2003) A constrained, force-directed layout algorithm for biological pathways. In: Liotta G (ed) Proc. International Symposium on Graph Drawing (GD'03), vol 2912. Springer LNCS, Heidelberg, pp 314–319
Klukas C, Schreiber F, Schwöbbermeyer H (2006) Coordinated perspectives and enhanced force-directed layout for the analysis of network motifs. In: Misue K, Sugiyama K, Tanaka J (eds) Proc. Asia-Pacific symposium on information visualization (APVis'06), CRPIT 60, pp 39–48
Friedrich C, Schreiber F (2003) Visualization and navigation methods for typed protein-protein interaction networks. Appl Bioinformatics 2(3):19–24
Junker BH, Koschützki D, Schreiber F (2006) Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 7:219
Le Novère N, Hucka M, Mi HY, Moodie S, Schreiber F, Sorokin A et al (2009) The systems biology graphical notation. Nat Biotechnol 27:735–741
Moodie S, Le Novère N, Sorokin A, Mi H, Schreiber F (2009) The Systems Biology Graphical Notation: process description language level 1. Nature Precedings 2009.3721
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H (2009) Systems biology graphical notation: entity relationship language level 1. Nature Precedings 2009.3719
Huaiyu M, Schreiber F, Le Novère N, Moodie S, Sorokin A (2009) Systems biology graphical notation: activity flow language level 1. Nature Precedings 2009.3724
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G et al (2014) The Reactome pathway knowledgebase. Nucleic Acids Res 42(1):D472–D477
Mi H, Muruganujan A, Thomas PD (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41(1):D377–D386
Chelliah V, Laibe C, Le Novère N (2013) BioModels database: a repository of mathematical models of biological processes. Methods Mol Biol 1021:189–199
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T et al (2013) Large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol 7:116
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S (2012) MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res 40(1):D1173–D1177
Junker A, Hartmann A, Schreiber F, Bäumlein H (2010) An engineer’s view on regulation of seed development. Trends Plant Sci 15(6):303–307
Czauderna T, Klukas C, Schreiber F (2010) Editing, validating, and translating of SBGN maps. Bioinformatics 26(18):2340–2341
Bar-Joseph Z, Gifford DK, Jaakkola TS (2001) Fast optimal leaf ordering for hierarchical clustering. Bioinformatics 17(Suppl 1):S22–S29
Biedl T, Brejová B, Demaine ED, Hamel AM, Vinař T (2001) Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data. Technical report 2001–14, Dept. of Computer Science, University of Waterloo
Di Battista G, Eades P, Tamassia R, Tollis IG (1999) Graph drawing. Prentice-Hall, Upper Saddle River, NJ
Eades P (1984) A heuristic for graph drawing. Congr Numer 42:149–160
Fruchterman T, Reingold E (1991) Graph drawing by force-directed placement. Software Pract Exper 21:1129–1164
Kamada T, Kawai S (1989) An algorithm for drawing general undirected graphs. Inf Process Lett 31:7–15
Sugiyama K, Misue K (1995) Graph drawing by magnetic spring model. J Vis Lang Comput 6(3):217–231
Madadhain J, Fisher D, Smyth P, White S, Boey YB (2005) Analysis and visualization of network data using JUNG. J Stat Softw 10:1–35
Bachmaier C, Brandenburg FJ, Forster M, Holleis P, Raitner M (2005) Gravisto: graph visualization toolkit. In: Pach J (ed) Proc. International Symposium on Graph Drawing (GD'04), vol 3383. Springer LNCS, Heidelberg, pp 502–503
Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F (2012) VANTED v2: a framework for systems biology applications. BMC Syst Biol 6(1):139
Junker A, Sorokin A, Czauderna T, Schreiber F, Mazein A (2012) Wiring diagrams in biology: towards the standardized representation of biological information. Trends Biotechnol 30(11):555–557
Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F (2012) Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat Protoc 7:579–593
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Czauderna, T., Schreiber, F. (2017). Information Visualization for Biological Data. In: Keith, J. (eds) Bioinformatics. Methods in Molecular Biology, vol 1526. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6613-4_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6613-4_21
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6611-0
Online ISBN: 978-1-4939-6613-4
eBook Packages: Springer Protocols