SpRay: A visual analytics approach for gene expression data

VAST 09 - IEEE Symposium on Visual Analytics Science and Technology, Proceedings

Volumn , Issue , 2009, Pages 179-186

  Dietzsch, Janko ^a   Heinrich, Julian ^b   Nieselt, Kay ^a   Bartz, Dirk ^c  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF STUTTGART   (Germany)

^c UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Bioinformatics; Gene expression experiments; Large scale microarray; Microarray data; Visual analytics

Indexed keywords

APPLICATION DOMAINS; BIOINFORMATICS APPLICATIONS; DATA SETS; GENE EXPRESSION DATA; GENE EXPRESSION DATASETS; HIGH-DIMENSIONAL; LARGE-SCALE MICROARRAY; MICROARRAY DATA; MICROARRAY EXPERIMENTS; NEW APPLICATIONS; PARALLEL COORDINATES; VISUAL ANALYSIS; VISUAL ANALYTICS; VISUAL EXPLORATION;

BIOACTIVITY; EXPERIMENTS; GENE EXPRESSION; GRAPHICAL USER INTERFACES; VISUALIZATION;

BIOINFORMATICS;

EID: 72849131352     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/VAST.2009.5333911     Document Type: Conference Paper

References (30)

1. D. Allison, X. Cui, G. Page, and M. Sabripour. Microarray Data Analysis: From Disarray to Consolidation and Consensus. Nature Reviews Genetics, 7(1):55-65, Jan 2006.
2. A. Artero, F. de Oliveira, and H. Levkowitz. Uncovering Clusters in Crowded Parallel Coordinates Visualization. In Proc. of IEEE Symposium on Information Visualization, pages 81-88, 2004.
3. D. Borland and R. Taylor II. Rainbow Color Map (Still) Considered Harmful. IEEE Computer Graphics and Applications, 27(2):14-17, 2007.
4. H. Doleisch, M. Gasser, and H. Hauser. Interactive Feature Specification for Focus+Context Visualization of Complex Simulation Data. In Proc. of EG/IEEE VGTC Symposium on Visualization, pages 239-248, 2003.
5. G. Ellis and A. Dix. Enabling Automatic Clutter Reduction in Parallel Coordinate Plots. IEEE Transactions on Visualization and Computer Graphics (Proc. of InfoVis), 12(5):717-723, 2008.
6. Y. Fua, M. Ward, and E. Rundensteiner. Hierarchical Parallel Coordinates for Visualizing Large Multivariate Data Sets. In Proc. of IEEE Visualization, pages 43-50, 1999.
7. N. Gehlenborg, J. Dietzsch, and K. Nieselt. Framework for Visualization of Microarray Data and Integrated Meta Information. Information Visualization, 4(3):164-175, 2005.
8. D. Gilbert, M. Schroeder, and J. van Helden. Interactive Visualization and Exploration of Relationships between Biological Objects. Trends in Biotechnology, 18(12):487-494, 2000.
9. S. Havre, M. Singhal, D. Payne, and B. Webb-Robertson. PQuad: Visualization of Predicted Peptides and Proteins. In Proc. of IEEE Visualization, pages 473-480, 2004.
10. J. Hong, D. Jeong, C. Shaw, et al. GVis: A Scalable Visualization Framework for Genomic Data. In Proc. of EG/IEEE VGTC Symposium on Visualization, pages 191-198, 2005.
11. A. Inselberg. The Plane with Parallel Coordinates. The Visual Computer, 1:69-92, 1985.
12. J. Johansson and M. Cooper. A Screen Space Quality Method for Data Abstraction. Computer Graphics Forum (Proc. of EuroVis), 27(3):1039-1046, 2008.
13. J. Johansson, P. Ljung, M. Jern, and M. Cooper. Revealing Structure within Clustered Parallel Coordinates Displays. In Proc. of IEEE Symposium on Information Visualization, pages 125-132, 2005.
14. F. Li, D. Bartz, L. Gu, and M. Audette. An Iterative Classification Method of 2D CT Head Data Based on Statistical and Spatial Information. In Proc. of International Conference on Pattern Recognition, 2008.
15. L. Linsen, J. Löcherbach, M. Berth, and J. Bernhardt. Differential Protein Expression Analysis via Liquid-Chromatography/Mass-Spectrometry Data Visualization. In Proc. of IEEE Visualization, pages 447-454, 2005.
16. K. McDonnell and K. Mueller. Illustrative Parallel Coordinates. Computer Graphics Forum (Proc. of EuroVis), 27(3):1031-1038, 2008.
17. M. Novotný and H. Hauser. Outlier-preserving Focus+Context Visualization in Parallel Coordinates. In Proc. of IEEE Visualization, pages 893-900, 2006.
18. T. Peeters, H. van de Wetering, M. Fiers, and J. van Wijk. Case Study: Visualization of Annotated DNA Sequences. In Proc. of EG/IEEE VGTC Symposium on Visualization, pages 109-114, 2004.
19. K. Pradhan, D. Bartz, and K. Mueller. SignatureSpace: A Multidimensional, Exploratory Approach for the Analysis of Volume Data. Technical Report WSI-2005-11, ISSN 0946-3852, Dept. of Computer Science (WSI), University of Tübingen, 2005.
20. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2007. ISBN 3-900051-07-0.
21. T. Rhyne, T. Dunning, G. Calapristi, et al. Panel 4: Evolving Visual Metaphors and Dynamic Tools for Bioinformatics Visualization. In Panel 4, IEEE Visualization, pages 579-582, 2002.
22. O. Rübel, G. Weber, S. Keränen, et al. PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates. In Proc. of EG/IEEE VGTC Symposium on Visualization, pages 203-210, 2006.
23. P. Saraiya, C. North, and K. Duca. Visualizing Biological Pathways: Requirements Analysis, Systems Evaluation and Research Agenda. In Proc. of IEEE Symposium on Information Visualization, pages 191-205, 2005.
24. K. Shedden and S. Cooper. Analysis of Cell-Cycle Gene Expression in Saccharomyces Cerevisiae Using Microarrays and Multiple Synchronization Methods. Nucleic Acids Research, 30(13):2920-2929, 2002.
25. P. Spellman, G. Sherlock, M. Zhang, et al. Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization. Molecular Biology of the Cell, 9(12):3273-3297, 1998.
26. D. Swayne, D. Lang, A. Buja, and D. Cook. GGobi: Evolving from XGobi into an Extensible Framework for Interactive Data Visualization. Computational Statistics & Data Analysis, 43:423-444, 2003.
27. E. Wegman and Q. Luo. High Dimensional Clustering Using Parallel Coordinates and the Grand Tour. Computing Science and Statistics, 28:361-368, 1997.
28. M. Westenberg, S. van Hijum, O. Kuipers, and J. Roerdink. Visualizing Genome Expression and Regulatory Network Dynamics in Genomics and Metabolic Context. Computer Graphics Forum (Proc. of EuroVis), 27(3):887-894, 2008.
29. H. Zhou, X. Yuan, H. Qu, et al. Visual Clustering in Parallel Coordinates. Computer Graphics Forum (Proc. of EuroVis), 27(3):1047-1054, 2008.
30. D. Zieker, E. Fehrenbach, J. Dietzsch, et al. cDNA Microarray Analysis Reveals Novel Candidate Genes Expressed in Human Peripheral Blood Following Exhaustive Exercise. Physiological Genomics, 23(3):287-294, 2005.