Caleydo: Design and evaluation of a visual analysis framework for gene expression data in its biological context

IEEE Pacific Visualization Symposium 2010, PacificVis 2010 - Proceedings

Volumn , Issue , 2010, Pages 57-64

  Lex, Alexander ^a   Streit, Marc ^a   Kruijff, Ernst ^a   Schmalstieg, Dieter ^a  

^a GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

Author keywords

Bioinformatics; Gene expression; Linking brushing; Multiple views; Pathways; Visual analysis

Indexed keywords

BIOLOGICAL PROCESS; COMPLEX NETWORKS; CONTEXTUAL INFORMATION; EVALUATION RESULTS; GENE EXPRESSION ANALYSIS; GENE EXPRESSION DATA; HYPOTHESES GENERATION; INTERACTIVE VISUALIZATIONS; LARGE DATASETS; LARGE NETWORKS; LIFE-SCIENCES; MULTIPLE INSTANCES; MULTIPLE PATHWAYS; MULTIPLE VIEWS; MULTIPLE-VIEW; ONLINE DATABASE; SPATIAL ORGANIZATION; SUBGRAPHS; VISUAL ANALYSIS;

BIOINFORMATICS; GENE EXPRESSION; VISUALIZATION;

GENE EXPRESSION REGULATION;

EID: 77951694233     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/PACIFICVIS.2010.5429609     Document Type: Conference Paper

References (24)

1. A. Aris and B. Shneiderman. Designing semantic substrates for visual network exploration. Information Visualization, 6(4):281-300, 2007.
2. M. Asslaber and K. Zatloukal. Biobanks: transnational, European and global networks. Brief Funct Genomic Prot., 6(3):193-201, 2007.
3. B. Stolk et al. Mining the human genome using virtual reality. In EGPGV '02: Proceedings of the Fourth Eurographics Workshop on Parallel Graphics and Visualization, pages 17-21, Aire-la-Ville, Switzerland, 2002.
4. M. Q. W. Baldonado, A. Woodruff, and A. Kuchinsky. Guidelines for using multiple views in information visualization. In AVI '00: Proceedings on Advanced visual interfaces, pages 110-119, New York, NY, USA, 2000. ACM Press.
5. T. Ball and S. G. Eick. Software visualization in the large. Computer, 29(4):33-43, 1996.
6. A. Barsky, T. Munzner, J. Gardy, and R. Kincaid. Cerebral: Visualizing multiple experimental conditions on a graph with biological context. Visualization and Computer Graphics, IEEE Transactions on, 14(6):1253-1260, Nov.-Dec. 2008.
7. C. Collins and S. Carpendale. Vislink: Revealing relationships amongst visualizations. IEEE Transactions on Visualization and Computer Graphics, 13(6):1192-1199, 2007.
8. M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Academy of Science USA, 95(25):14863-14868, December 1998.
9. B. J. J. Frey and D. Dueck. Clustering by passing messages between data points. Science, 315(5814):972-976, January 2007.
10. H. Chung et al. Arrayxpath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using scalable vector graphics. Nucleic Acids Res, 33(Web Server issue):W621-W626, Jul 2005.
11. M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi. Kegg for linking genomes to life and the environment. Nucleic Acids Research, 36(Database-Issue):480-484, 2008.
12. C. Klukas and F. Schreiber. Dynamic exploration and editing of kegg pathway diagrams. Bioinformatics, 23(3):344-350, 2006.
13. H. Lindroos and S. G. E. Andersson. Visualizing metabolic pathways: comparative genomics and expression analysis. In Proceedings of the IEEE, volume 90, pages 1793-1802, 2002. (Pubitemid 43758725)
14. J. D. Mackinlay, G. G. Robertson, and S. K. Card. The perspective wall: detail and context smoothly integrated. In CHI 1991: Proceedings on Human factors in computing systems, pages 173-176, New York, NY, USA, 1991. ACM Press.
15. B. Mlecnik, M. Scheideler, H. Hackl, J. Hartler, F. Sanchez-Cabo, and Z. Trajanoski. Pathwayexplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Research, 33(Web Server issue):633-637, July 2005.
16. H. Mueller, R. Reihs, S. Sauer, K. Zatloukal, M. Streit, L. Alexander, B. Schlegl, and D. Schmalstieg. Connecting genes with diseases. In Sixth International Conference BioMedical Visualization, 2009.
17. O. Rübel et al. Pointcloudxplore: Visual analysis of 3d gene expression data using physical views and parallel coordinates. In EuroVis, pages 203-210. Eurographics Association, 2006.
18. G. Schmidt-Gann, K. Schmid, M. Uehlein, J. Struck, A. Bergmann, D. Schmalstieg, M. Streit, A. Lex, D. G. van der Nest, M. van Griensven, and H. Redl. Gene- and protein expression profiling in liver in a sepsis-baboon model. In 32nd Annual Meeting on Shock, San Antonio, Texas, June 6-9, 2009.
19. J. Seo and B. Shneiderman. A rank-by-feature framework for interactive exploration of multidimensional data. Information Visualization, 4(2):96-113, 2005.
20. B. Shneiderman and A. Aris. Network visualization by semantic substrates. IEEE Transactions on Visualization and Computer Graphics, 12(5):733-740, 2006.
21. M. Streit, M. Kalkusch, K. Kashofer, and D. Schmalstieg. Navigation and exploration of interconnected pathways. Computer Graphics Forum (EuroVis 2008), 27(3):951-958(8), May 2008.
22. M. Streit, A. Lex, H. Müller, and D. Schmalstieg. Gaze-based interaction for information visualization. In Proceedings of web3DW 2009 Conference, Algarve, Portugal, 2009.
23. Y. Yang, E. S. Wurtele, C. Cruz-Neira, and J. A. Dickerson. Hierarchical visualization of metabolic networks using virtual reality. In VRCIA '06: Proceedings on Virtual reality continuum and its applications, pages 377-381, New York, NY, USA, 2006. ACM Press.
24. B. Yost, Y. Haciahmetoglu, and C. North. Beyond visual acuity: the perceptual scalability of information visualizations for large displays. In CHI '07: Proceedings of the SIGCHI conference on Human factors in computing systems, pages 101-110, New York, NY, USA, 2007.