Abstract
Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila TranscriptionNetwork Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point- Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions.We address this challenge by linking PCX and Matlab® via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.
MATLAB is a registered trademark of The MathWorks Inc., 3 Apple Hill Drive Natick, MA 01760-2098, USA. Online at: http://www.mathworks.com/
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
L. P. Andrioli, V. Vasisht, E. Theodosopoulou, A. Oberstein, and S. Small. Anterior repressionof a Drosophila stripe enhancer requires three position-specific mechanisms. Development,129 (21):4931–4940, November 2002.
M. Q. W. Baldonado, A. Woodruff, and A. Kuchinsky. Guidelines for using multiple viewsin information visualization. In AVI ’00: Proceedings of the working conference on Advancedvisual interfaces, 110–119, New York, NY, USA, 2000. ACM Press.
L. D. Davis and M. Mitchell. Handbook of genetic algorithms. Van Nostrand Reinhold, 1991.
H. De Jong. Modeling and simulation of genetic regulatory systems: A literature review.Journal of Computational Biology, 9(1):67–103, 2002.
P. D’haeseleer, S. Liang, and R. Somogyi. Genetic network inference: from co-expressionclustering to reverse engineeing. Bioinformatics, 16(8):707–726, 2000.
H. Doleisch, M. Gasser, and H. Hauser. Interactive feature specification for focus C contextvisualization of complexsimulation data. In G.-P. Bonneau, S. Hahmann, and C. D. Hansen,editors, Data Visualization 2003 (Proceedings of the Eurographics/IEEE TCVG SymposimonVisualization), 2003.
C. C. Fowlkes, C. L. L. Hendriks, S. V. E. Keränen, G. H. Weber, O. R übel, M.-Y. Huang,S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker,B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, and J. Malik. A quantitativespatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell, 133:364–374, April 2008.
M. Fujioka, P. Miskiewicz, L. Raj, A. A. Gulledge, M. Weir, and T. Goto. Drosophila pairedregulates late even-skipped expression through a composite binding site for the paired domainand the homeodomain. Development, 122(9):2697–2707, Sept. 1996.
D. L. Gresh, B. E. Rogowitz, R. L. Winslow, D. F. Scollan, and C. K. Yung. WEAVE:A system for visually linking 3-d and statistical visualizations,applied to cardiac simulationand measurement data. In T. Ertl, B. Hamann, and A. Varshney, editors, Proceedings IEEE Visualization 2000, 489–492, Los Alamitos, CA, USA, 2000. IEEE Computer Society Press.
U. Grossniklaus, K. M. Cadigan, and W. J. Gehring. Three maternal coordinate systems cooperate in the patterning of the Drosophila head. Development, 120(11):3155–3171, 1994.
E. E. Hare, B. K. Perterson, V. N. Iyer, R. Meier, and M. B. Eisen. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genetics, 4(6):e1000106., 2008.
C. Henze. Feature detection in linked derived spaces. In D. Ebert, H. Rushmeier, and H. Hagen, editors, Proceedings IEEE Visualization ’98, 87–94, Los Alamitos, CA, USA, 1998. IEEE Computer Society Press.
M.-Y. Huang, O. R übel, G. H. Weber, C. L. Luengo Hendriks, M. D. Biggin, H. Hagen, and B. Hamann. Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos, 313–327. Springer Verlag, Germany, Jan 2008.
J. Jaeger, M. Blagov, D. Kosman, K. N. Kozlov, Manu, E. Myasnikova, S. Surkova, C. E.Vanario-Alonso, M. Samsonova, D. H. Sharp, and J. Reinitz. Dynamical analysis of regulatoryinteractions in the Gap gene system of Drosophila melanogaster. Genetics, 167(4):1721–1757,April 2004.
H. Janssens, S. Hou, J. Jaeger, A.-R. Kim, E. Myasnikova, D. Sharp, and J. Reinitz. Quantitativeand predictive model of transcriptional control of the Drosophila melanogaster even skippedgene. Nature Genetics, 38, Sept. 2006.
C. Johnson, S. G. Parker, C. Hansen, G. L. Kindlmann, and Y. Livnat. Interactive simulationand visualization. Computer, 32(12):59–65, December 1999.
R. Kraut and M. Levine. Spatial regulation of the gap gene giant during Drosophila develop-ment. Development, 111(2):601–609, 1991.
D. T. Lang and D. F. Swayne. GGobi meets R: an extensible environment for interactivedynamic data visualization. In Proceedings of the 2nd International Workshop on DistributedStatistical Computing, Mar. 2001.
C. L. Luengo Hendriks, S. V. E. Keränen, C. C. Fowlkes, L. Simirenko, G. H. Weber, A. H. DePace, C. Henriquez, D. W. Kaszuba, B. Hamann, M. B. Eisen, J. Malik, D. Sudar, M. D. Biggin, and D. W. Knowles. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: Data acquisition pipeline. Genome Biology, 7 (12):R123, 2006.
O. R übel, G. H. Weber, M.-Y. Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. L. Hendriks, S. V. E. Keränen, M. B. Eisen, D. W. Knowles, J. Malik, H. Hagen, and B. Hamann. Integrating data clustering and visualization for the analysis of 3d gene expression data. IEEE Transactions on Computational Biology and Bioinformatics, 2008.
S. R. Russell, N. Sanchez-Soriano, C. Wright, and M. Ashburner. The Dichaete gene ofDrosophila melanogaster encodes a SOX-domain protein required for embryonic segmentation. Development, 122(11):3669–3676, 1996.
F. Sauer and H. Jäckle. Heterodimeric Drosophila gap gene protein complexes acting astranscriptional repressors. EMBO Journal, 14(19):4773–4780, 1995.
S. Small, A. Blair, and M. Levine. Regulation of even-skipped stripe 2 in the Drosophila embryo. The EMBO journal, 11(11):4047–4057, Nov. 1992.
S. Small, A. Blair, and M. Levine. Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. Developmental Biology, 175(2):314–324, May 1996.
S. Small, R. Kraut, T. Hoey, R. Warrior, and M. Levine. Transcriptional regulation of a pair-rule stripe in Drosophila. Genes Dev, 5(5):827–839, May 1991.
D. Thieffry and L. Sanchez. Dynamical modeling of pattern formation during embryonic development. Current opinion in genetics & development, 13(4):326–330, 2003.
E. P. van Someren, L. F. A. Wessels, E. Backer, and M. J. T. Reinders. Genetic network modeling. Pharmacogenomics, 3(4):507–525, 2002.
G. H. Weber, O. Rübel, M.-Y. Huang, A. DePace, C. C. Fowlkes, S. V. Ker änen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin, and B. Hamann. Visual exploration of three-dimensional gene expression using physical views and linked abstractviews. IEEE Transactions on Computational Biology and Bioinformatics, 6(2):296–309, April-June 2009.
D. Whitley. A genetic algorithm tutorial. Statistics and Computing, 4(2):65–85, June 1994.
R. Yan, S. Small, C. Desplan, C. R. Dearolf, and J. E. Darnell Jr. Identification of a Stat genethat functions in Drosophila development. Cell, 84(3):421–430, Feb 1996.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rübel, O. et al. (2012). Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data. In: Linsen, L., Hagen, H., Hamann, B., Hege, HC. (eds) Visualization in Medicine and Life Sciences II. Mathematics and Visualization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21608-4_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-21608-4_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21607-7
Online ISBN: 978-3-642-21608-4
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)