Abstract
Gene expression data studies are often concerned with comparing experimental versus control conditions. Ratios of gene expression values, fold changes, are therefore commonly used as biologically meaningful markers. Visual representations are inevitable for the explorative analysis of data. Fold changes alone are no reliable markers, since low signal intensities may lead to unreliable ratios and should therefore be visually marked less important than the more trustworthy ratios of larger expression values.
Methods: We propose a new visualization scheme showing ratios and their confidence together in one single diagram, enabling a more precise explorative assessment of gene expression data. Basis of the visualization scheme are near-uniform perceptible color scales improving the readability of the commonly used red-green color scale. A sub-sampling algorithm for optimizing color scales is presented. Instead of difficult to read bivariate color maps encoding two variables into a single color we propose the use of colored patches (rectangles) of different sizes representing the absolute values, while representing ratios by a univariate color map. Different pre-processing steps for visual bandwidth limitation and reliability value estimation are proposed.
Results and Conlusions: The proposed bivariate visualization scheme shows a clear perceptible order in ratio and reliability values leading to better and clearer interpretable diagrams. The proposed color scales were specifically adapted to human visual perception. Psychophysical optimized color scales are superior to traditional sRGB red-green maps. This leads to an improved explorative assessment of gene expression data.
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References
Eisen, M., Spellman, P., Brown, P., Botstein, D.: Cluster analysis and display of genome-wide expression patterns. PNAS 95, 14863–14868 (1998)
Ware, C.: Information Visualization, 2nd edn. Morgan Kaufmann, San Francisco (2004)
Spence, I., Efendov, A.: Target detection in scientific visualization. Journal of Exp. Psych.: App. 7, 13–26 (2001)
Wit, E., McClure, J.: Statistics for Microarrays. Wiley, Chichester (2004)
CIE: Colorimetry, 3rd edn., Technical report, Commission Internationale de l’Eclairage, CIE 15 2004 (2004)
Levkowitz, H.: Color theory and modeling for computer graphics, visualization, and multimedia applications. Kluwer, Dordrecht (1997)
Stokes, M., Anderson, M., Chandrasekar, S., Motta, R.: A standard default color space for the internet - srgb. Technical report, W3C - World Wide Web Consortium (1996)
ICC: Image technology colour management - architecture, profile format, and data structure. Technical Report ICC.1:2004-10, International Color Consortium (2004)
IEC: Multimedia systems and equipment - colour measurement and management - part 2-1: Colour management - default rgb colour space - srgb. Technical report, International Electrotechnical Commission, IEC 61966-2-1 (1999)
Hoffmann, G.: Cie color space. Technical report, FH Emden, Germany (2005)
Robertson, P.K., O’Callaghan, J.F.: The generation of color sequences for univariate and bivariate mapping. IEEE Computer Graphics and Applications 6, 24–32 (1986)
Fensterer, H., Giehl, K., Buchholz, M., Ellenrieder, V., Buck, A., Kestler, H., Adler, G., Gierschik, P., Gress, T.: Expression profiling of the influence of ras mutants on the tgfb1-induced phenotype of the pancreatic cancer cell line panc-1. Genes Chromosomes Cancer 39, 224–235 (2004)
Stone, M.C., Cowan, W.B., Beatty, J.C.: Color gamut mapping and the printing of digital color images. ACM Trans. Graph. 7, 249–292 (1988)
Stone, M.C.: Color printing for computer graphics. In: Rogers, D.F., Earnshaw, R.A. (eds.) Computer Graphics Techniques - Theory and Practice, pp. 79–127. Springer, Heidelberg (1990)
Strimmer, K.: Modeling gene expression measurement error: a quasi-likelihood approach. BMC Bioinformatics 4, 10 (2003)
Ware, C.: Color sequences for univariate maps: Theory, experiments and principles. IEEE Comput. Graph. Appl. 8, 41–49 (1988)
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Kestler, H.A., Müller, A., Buchholz, M., Gress, T.M., Palm, G. (2006). A Perceptually Optimized Scheme for Visualizing Gene Expression Ratios with Confidence Values. In: André, E., Dybkjær, L., Minker, W., Neumann, H., Weber, M. (eds) Perception and Interactive Technologies. PIT 2006. Lecture Notes in Computer Science(), vol 4021. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11768029_8
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DOI: https://doi.org/10.1007/11768029_8
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