Visualizing uncertainty in biological expression data

Proceedings of SPIE - The International Society for Optical Engineering

Volumn 8294, Issue , 2012, Pages

  Holzhüter, Clemens ^a   Lex, Alexander ^b   Schmalstieg, Dieter ^b   Schulz, Hans Jörg ^b   Schumann, Heidrun ^a   Streit, Marc ^c  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^c JOHANNES KEPLER UNIVERSITY LINZ   (Austria)

Author keywords

Expression Data; Uncertainty; Visualization

Indexed keywords

ERROR THRESHOLD; EXPRESSION ANALYSIS; EXPRESSION DATA; GENERAL APPROACH; HEATMAPS; LIFE-SCIENCES; STANDARD PROCEDURES; TECHNICAL LIMITATIONS; UNCERTAIN DATAS; UNCERTAINTY; UNIVERSITY OF GRAZ; VISUAL FEEDBACK; VISUAL REPRESENTATIONS;

FLOW VISUALIZATION; UNCERTAINTY ANALYSIS; VISUAL COMMUNICATION; VISUALIZATION;

DATA VISUALIZATION;

EID: 84857003391     PISSN: 0277786X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.908516     Document Type: Conference Paper

References (30)

1. Mayer, B., ed., [Bioinformatics for Omics Data - Methods and Protocols ], no. 719 in Methods in Molecular Biology, Springer (2011).
2. Shneiderman, B., "The eyes have it: A task by data type taxonomy for information visualizations," in [Proceedings of the IEEE Symposium on Visual Languages (VL '96) ], 336-343 (1996).
3. O'Donoghue, S., Gavin, A., Gehlenborg, N., Goodsell, D., Hériché, J., Nielsen, C., North, C., Olson, A., Procter, J., Shattuck, D., Walter, T., and Wong, B., "Visualizing biological data-now and in the future," Nature Methods 7(3s), 2-4 (2010).
4. Hunter, G. J. and Goodchild, M. F., "Managing uncertainty in spatial databases: Putting theory into practice," URISA Journal 5(2), 55-62 (1993). (Pubitemid 24401593)
5. Griethe, H. and Schumann, H., "The visualization of uncertain data: Methods and problems," in [Proceedings of the Simulation and Visualization (SimVis '06)], 143-156, SCS Publishing House (2006).
6. Skeels, M., Lee, B., Smith, G., and Robertson, G., "Revealing uncertainty for information visualization," in [Proceedings of the Conference on Advanced Visual Interfaces (AVI '08) ], 376-379, ACM Press (2008).
7. Wittenbrink, C. M., Pang, A. T., and Lodha, S. K., "Glyphs for visualizing uncertainty in vector fields," IEEE Transactions on Visualization and Computer Graphics 2(3), 266-279 (1996). (Pubitemid 126781407)
8. Olston, C. and Mackinlay, J. D., "Visualizing data with bounded uncertainty," in [Proceedings of the IEEE Symposium on Information Visualization (InfoVis '02)], 37-40, IEEE Computer Society Press (2002).
9. Streit, A., Pham, B., and Brown, R., "A spreadsheet approach to facilitate visualization of uncertainty in information," IEEE Transactions on Visualization and Computer Graphics 14(1), 61-72 (2008). (Pubitemid 350157880)
10. Potter, K., Kniss, J., Riesenfeld, R., and Johnson, C., "Visualizing summary statistics and uncertainty," Computer Graphics Forum 29(3), 823-832 (2010).
11. Zuk, T. and Carpendale, S., "Theoretical analysis of uncertainty visualizations," in [Proceedings of the Conference on Visualization and Data Analysis (VDA '06)], 6060, 66-79, IS&T/SPIE (2006).
12. Pang, A. T., Wittenbrink, C. M., and Lodh, S. K., "Approaches to uncertainty visualization," The Visual Computer 13(8), 370-390 (1997). (Pubitemid 127583168)
13. MacEachren, A. M., Robinson, A., Hopper, S., Gardner, S., Murray, R., Gahegan, M., and Hetzler, E., "Visualizing geospatial information uncertainty: What we know and what we need to know.," Cartography and Geographic Information Science 32(3), 139-161 (2005).
14. Zbilut, J. P. and Giuliani, A., "Biological uncertainty," Theory in Biosciences 127(3), 223-227 (2008).
15. Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S. B., and Bassett, D. E., "Rosetta error model for gene expression analysis," Bioinformatics 22(9), 1111-1121 (2006).
16. Nielsen, C. B., Cantor, M., Dubchak, I., Gordon, D., and Wang, T., "Visualizing genomes: techniques and challenges," Nature Methods 7(3s), S5-S15 (2010).
17. Lundström, C., Ljung, P., Persson, A., and Ynnerman, A., "Uncertainty visualization in medical volume rendering using probabilistic animation," IEEE Transactions on Visualization and Computer Graphics (Vis '07) 13(6), 1648-1655 (2007). (Pubitemid 350076644)
18. Pearson, R. D., Liu, X., Sanguinetti, G., Milo, M., Lawrence, N. D., and Rattray, M., "puma: a bioconductor package for propagating uncertainty in microarray analysis," BMC Bioinformatics 10(211) (2009).
19. Holzhüter, C., Schulz, H., and Schumann, H., "Enriched heatmaps for visualizing uncertainty in microarray data," in [Poster at the Eurographics Workshop on Visual Computing for Biomedicine (VCBM '10)], (2010).
20. Wang, X., Ghosh, S., and Guo, S. W., "Quantitative quality control in microarray image processing and data acquisition," Nucleic Acids Research 29(15), e75 (2001).
21. Tominski, C. and Schumann, H., "Visualization of gene combinations," in [Proceedings of the Conference on Information Visualisation (IV '08)], 120-126, IEEE Computer Society Press (2008).
22. Ellis, G. and Dix, A., "The plot, the clutter, the sampling and its lens," in [Proceedings of the Conference on Advanced Visual Interfaces (AVI '06)], 266-269, ACM Press (2006).
23. Tufte, E. R., [The Visual Display of Quantitative Information], Graphics Press, Cheshire, Coneeticut, 2nd ed. (1983).
24. He, Z. and Zhou, J., "Empirical evaluation of a new method for calculating Signal-to-Noise ratio for microarray data analysis," Applied and Environmental Microbiology 74(10), 2957-2966 (2008). (Pubitemid 351746997)
25. Hall, P. and Selinger, B., "Statistical significance: Balancing evidence against doubt," Australian Journal of Statistics 28(3), 354-370 (1986).
26. Pounds, S. and Morris, S. W., "Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values," Bioinformatics 19(10), 1236-1242 (2003). (Pubitemid 36850216)
27. Geymayer, T., Lex, A., Streit, M., and Schmalstieg, D., "Visualizing the effects of logically combined filters," in [Proceedings of the Conference on Information Visualisation (IV '11) ], IEEE Computer Society Press (2011).
28. Lex, A., Streit, M., Partl, C., Kashofer, K., and Schmalstieg, D., "Comparative analysis of multidimensional, quantitative data," IEEE Transactions on Visualization and Computer Graphics (InfoVis '10) 16(6), 1027-1035 (2010).
29. Lex, A., Streit, M., Kruijff, E., and Schmalstieg, D., "Caleydo: Design and evaluation of a visual analysis framework for gene expression data in its biological context," in [Proceeding of the IEEE Symposium on Pacific Visualization (PacificVis '10)], 57-64, IEEE Computer Society Press (2010).
30. Oelke, D., Janetzko, H., Simon, S., Neuhaus, K., and Keim, D. A., "Visual boosting in pixel-based visualizations," Computer Graphics Forum 30, 871-880 (2011).