Linking advanced visualization and Matlab for the analysis of 3D gene expression data

Mathematics and Visualization

Volumn 0, Issue , 2012, Pages 265-283

  Rübel, Oliver ^a,b,c   Keränen, Soile V E ^a   Biggin, Mark ^a   Knowles, David W ^a   Weber, Gunther H ^a   Hagen, Hans ^c   Hamann, Bernd ^a,b,c   Bethel, E Wes ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b University of California   (United States)

^c Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; DATA VISUALIZATION; MATLAB; THREE DIMENSIONAL COMPUTER GRAPHICS; TRANSCRIPTION; VISUALIZATION;

ADVANCED VISUALIZATIONS; DROSOPHILA EMBRYOS; DROSOPHILLA; GENE EXPRESSION DATA; GENES EXPRESSION; POINT CLOUD DATA; QUANTITATIVE INFORMATION; SPATIAL EXPRESSIONS; TEMPORAL EXPRESSIONS; TRANSCRIPTION NETWORKS;

GENETIC ALGORITHMS;

EID: 84910038681     PISSN: 16123786     EISSN: 2197666X     Source Type: Book Series    
DOI: 10.1007/978-3-642-21608-4_15     Document Type: Conference Paper

References (30)

1. 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.
2. 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.
3. L. D. Davis and M. Mitchell. Handbook of genetic algorithms. Van Nostrand Reinhold, 1991.
4. H. De Jong. Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology, 9(1):67-103, 2002.
5. P. D’haeseleer, S. Liang, and R. Somogyi. Genetic network inference: from co-expressionclustering to reverse engineeing. Bioinformatics, 16(8):707-726, 2000.
6. 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.
7. C. C. Fowlkes, C. L. L. Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. De Pace, 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.
8. M. Fujioka, P. Miskiewicz, L. Raj, A. A. Gulledge, M. Weir, and T. Goto. Drosophilapairedregulates late even-skipped expression through a composite binding site for the paired domainand the homeodomain. Development, 122(9):2697-2707, Sept. 1996.
9. 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.
10. 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.
11. E. E. Hare, B. K. Perterson, V. N. Iyer, R. Meier, and M. B. Eisen. Sepsid even-skippedenhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genetics, 4(6):e1000106., 2008.
12. 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.
13. 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.
14. 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.
15. 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.
16. C. Johnson, S. G. Parker, C. Hansen, G. L. Kindlmann, and Y. Livnat. Interactive simulationand visualization. Computer, 32(12):59-65, December 1999.
17. R. Kraut and M. Levine. Spatial regulation of the gap gene giant during Drosophiladevelop-ment. Development, 111(2):601-609, 1991.
18. 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.
19. 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.
20. O. Rübel, 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.
21. 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.
22. F. Sauer and H. Jäckle. Heterodimeric Drosophila gap gene protein complexes acting astranscriptional repressors. EMBO Journal, 14(19):4773-4780, 1995.
23. S. Small, A. Blair, and M. Levine. Regulation of even-skipped stripe 2 in the Drosophilaembryo. The EMBO journal, 11(11):4047-4057, Nov. 1992.
24. 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.
25. 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.
26. D. Thieffry and L. Sanchez. Dynamical modeling of pattern formation during embryonic development. Current opinion in genetics & development, 13(4):326-330, 2003.
27. E. P. van Someren, L. F. A. Wessels, E. Backer, and M. J. T. Reinders. Genetic network modeling. Pharmacogenomics, 3(4):507-525, 2002.
28. G. H. Weber, O. Rübel, M.-Y. Huang, A. DePace, C. C. Fowlkes, S. V. Keränen, 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.
29. D. Whitley. A genetic algorithm tutorial. Statistics and Computing, 4(2):65-85, June 1994.
30. R. Yan, S. Small, C. Desplan, C. R. Dearolf, and J. E. Darnell Jr. Identification of a Statgenethat functions in Drosophila development. Cell, 84(3):421-430, Feb 1996.