Cerebral: Visualizing multiple experimental conditions on a graph with biological context

IEEE Transactions on Visualization and Computer Graphics

Volumn 14, Issue 6, 2008, Pages 1253-1260

  Barsky, Aaron ^a   Munzner, Tamara ^a   Gardy, Jennifer ^a   Kincaid, Robert ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b AGILENT LABORATORIES   (United States)

Author keywords

Design study; Graph layout; Small multiples; Systems biology visualization

Indexed keywords

COORDINATED VIEWS; DATA INFORMATIONS; DATASETS; DESIGN DECISIONS; DESIGN STUDY; EXPERIMENTAL CONDITIONS; EXPERIMENTAL DATUM; GRAPH LAYOUT; GRAPH LAYOUTS; GRAPH MODELS; INTERACTION GRAPHS; ITERATIVE PROCESSES; LIVING CELLS; MOLECULAR LEVELS; PARALLEL COORDINATES; SMALL MULTIPLES; SYSTEMS BIOLOGY VISUALIZATION;

BIOLOGICAL SYSTEMS; BIOLOGY; COORDINATION REACTIONS; EXPERIMENTS; FLOW INTERACTIONS; INFORMATION THEORY; ISOMERS; KNOWLEDGE BASED SYSTEMS; KNOWLEDGE REPRESENTATION; MODAL ANALYSIS; THEOREM PROVING;

GRAPH THEORY;

PROTEOME;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION;

BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 54949110152     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2008.117     Document Type: Conference Paper

References (42)

1. V. Akman, W. R. Franklin, M. Kankanhalli, and C. Narayanaswami. Geometric computing and the uniform grid data technique. Computer Aided Design, 21(7):410-420, 1989.
2. D. Auber, Tulip : A huge graph visualization framework. In P. Mutzel and M. Jünger, editors, Graph Drawing Software, Mathematics and Visualization, pages 105-126. Springer-Verlag, 2003.
3. M. Baitaluk, M. Sedova, A. Ray, and A. Gupta. BiologicalNetworks: visualization and analysis tool for systems biology. Nucl. Acids Res., 34(suppl_2):W466-471, 2006.
4. M. Q. W. Baldonado. A. Woodruff, and A. Kuchinsky. Guidelines for using multiple views in information visualization. In Proc. Advanced Visual Interface (AVI '00). pages 110-119, 2000.
5. A. Barsky, Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context. Master's thesis, University of British Columbia, Dept. Computer Science. Vancouver, June 2008.
6. A. Barsky, J. L. Gardy, R. E. Hancock, and T. Munzner. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 23(8): 1040-1042, 2007.
7. B.-J. Breitkreutz, C. Stark, and M. Tyers. Osprey: a network visualization system. Genome Biology, 4(3):R22, 2003.
8. J. E. Bresenham. Algorithm for computer control of a digital plotter. IBM Systems Journal. 4(1):25-30, 1965.
9. K. L. Brown, C. Cosseau, J. L. Gardy, and R. E. Hancock. Complexities of targeting innate immunity to treat infection. Trends in Immunology, 28(6):260-266, 2007.
10. K. Dahlquist et al. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet., 31:19-20, 2002.
11. R. Davidson and D. Harel. Drawing graphs nicely using simulated annealing. ACM Trans. on Graphics. 15(4):301-331, 1996.
12. U. de Lichtenberg, L. Jensen, S. Brunak, and P. Bork. Dynamic complex formation during the yeast cell cycle. Science, 307(5710):724-727, 2005.
13. A. Drawid and M. Gerstein. A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol., 301:1059-1075, 2000. http://bioinfo.mbb. yale.edu/genome/localize/.
14. T. Dwyer and K. Marriott. IPSep-CoLa: An incremental procedure for separation constraint layout of graphs. IEEE Trans. Visualization and Computer Graphics (Proc. InfoVis '06), 12(5):821-828, 2006.
15. M. D. Dyer, T. M. Murali, and B. W. Sobral. The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog, 4(2):e32, Feb 2008.
16. A. Frick, A. Ludwig, and H. Mehldau. A fast adaptive layout algorithm for undirected graphs. In Proc. Graph Drawing 1993 (GD03), LNCS 894, pages 388-403, Springer, 10-12 1994.
17. T. M. J. Fruchterman and E. M. Reingold. Graph drawing by force-directed placement. Software - Practice and Experience. 21(11): 1129-1164, 1991.
18. B. Genc and U. Dogrusoz. A constrained, force-directed layout algorithm for biological pathways. In Proc. Graph Drawing 2003 (GD'03), LNCS 2912, pages 314-319. Springer, 2004.
19. M. A. Harrower and C. A. Brewer. ColorBrewer.org: An online tool for selecting color schemes for maps. The Cartographic Journal, 40(1):27-37, 2003.
20. L. He et al. The glomerular transcriptome and a predicted protein-protein interaction network. J. Am. Soc. Nephrol., 19(2):260-268, 2008.
21. J. Heer, S. K. Card, and J. A. Landay, prefuse: a toolkit for interactive information visualization. In Proc. ACM CHI '05, pages 421-430, 2005.
22. Z. Hu, J. Mellor, J. Wu, and C. DeLisi, VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics, 5(1):17, 2004.
23. B. S. Jinwook Seo. Interactively exploring hierarchical clustering results. IEEE Computer, 35(7):80-86. 2002.
24. B. Junker, C. Klukas, and F. Schreiber. Vanted: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7(1): 109, 2006.
25. M. Kato, M. Nagasaki, A. Doi, and S. Miyano. Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform., 16(2):22-31, 2005.
26. K. Kojima, M. Nagasaki, E. Jeong, M. Kato, and S. Miyano. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics. 8:76+, March 2007.
27. W. Li and H. Kurata. A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics, 21(9):2036-2042, May 2005.
28. S. Maere, K. Heymans, and M. Kuiper. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21:3448-3449, 2005.
29. H. C. Mak, M. Daly, B. Gruebel, and T. Ideker. CellCircuits: a database of protein network models. Nucl. Acids Res., 35:D538D545, 2007, http://www.cellcircuits.org/.
30. N. Mookherjee et al. Modulation of the Toll-like receptor-mediated inflammatory response by the endogenous human host defence peptide LL37, J. Immunol., 176:2455-2464, 2006.
31. M. Plumlee and C. Ware. Zooming versus multiple window interfaces: Cognitive costs of visual comparisons. Proc. ACM Trans. on Computer-Human Interaction (ToCHI), 13(2): 179-209. 2006.
32. P. Saraiya, P. Lee, and C. North. Visualization of graphs with associated timeseries data. In IEEE Symp. Information Visualization (InfoVis 2005), pages 225-232, 2005.
33. P. Shannon et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research. 13:2498-2504, 2003.
34. B. Shneiderman and A. Aris. Network visualization by semantic substrates. IEEE Trans. Visualization and Computer Graphics, (Proc. InfoVis 2006), 12(5):733-740. 2006.
35. P. Spellman et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell, 9:3273-3297, 1998.
36. M. Suderman and M. Hallett. Tools for visually exploring biological networks. Bioinformatics. 23(20):2651-2659. 2007.
37. A. Sutton, J. Bucaria. M. A. Osley, and R. Sternglanz. Yeast ASF1 protein is required for cell cycle regulation of histone gene transcription. Genetics, 158:587596, 2001.
38. E. Tufte. Envisioning Information. Graphics Press, 1990.
39. D. Tunkelang. A practical approach to drawing undirected graphs. Technical Report CMU-CS-94-161, Carnegie Mellon University Department of Computer Science, June 1994.
40. B. Tversky, J. B. Morrison, and M. Betrancourt. Animation: can it facilitate? International Journal of Human-Computer Studies, 57(4):247-262, 2002.
41. M. A. Westenberg et al. Interactive visualization of gene regulatory networks with associated gene expression time series data. In Visualization in Medicine and Life Sciences, Visualization and Mathematics, pages 293-312, 2008.
42. K. Yeung, M. Medvedovic. and R. Bumgarner. Clustering geneexpression data with repeated measurements. Genome Biology, 4(5):R34, 2003.