Quantification of transcription factor expression from Arabidopsis images

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Mace, Daniel L ^a   Lee, Ji Young ^a   Twigg, Richard W ^a   Colinas, Juliette ^a   Benfey, Philip N ^a   Ohler, Uwe ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; AMINO ACID SEQUENCE; ARABIDOPSIS; AUTOMATION; CELL SELECTION; CONFERENCE PAPER; CONFOCAL MICROSCOPY; CONTROLLED STUDY; CORRELATION ANALYSIS; FLUORESCENCE ACTIVATED CELL SORTING; GENE MAPPING; GENETIC TRANSFORMATION; IMAGE ANALYSIS; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; NONHUMAN; PLANT CELL; PLANT GENETICS; PLANT ROOT; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REPORTER GENE; SCORING SYSTEM; VALIDATION PROCESS;

ARABIDOPSIS;

EID: 33747888338     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl228     Document Type: Conference Paper

References (26)

1. Bar-Joseph, Z. (2004) Analyzing time series gene expression data. Bioinformatics, 20, 2493-2503.
2. Benfey, P. N. and Scheres, B. (2000) Root development. Current Biology, 10, R813-R815.
3. Birnbaum, K., Shasha, D. E., Wang, J. Y., Jung, J. W., Lambert, G. M., Galbraith, D.W. and Benfey, P. N. (2003) A gene expression map of the Arabidopsis root. Science, 302, 1956-1960.
4. Bookstein, F. L. (1989) Principal warps: Thin-plate splines and the decomposition of deformations. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 11, 567-585.
5. Chenyang, X. and Prince, J. L. (1998) Snakes, shapes, and gradient vector flow. Image Processing, IEEE Transactions on, 7, 359-369.
6. Chudakov, D. M., Lukyanov, S. and Lukyanov, K. A. (2005) Fluorescent proteins as a toolkit for in vivo imaging. Trends in Biotechnology, 23, 605-613.
7. Dmochowski, I. J., Dmochowski, J. E., Oliveri, P., Davidson, E. H. and Fraser, S. E. (2002) Quantitative imaging of cis-regulatory reporters in living embryos. PNAS, 99, 12895-12900.
8. Dollar, P. (2006) Matlab TPS (Thin Plate Spline) implementation. http://vision.ucsd.edu/pdol-lar/toolbox/doc/index.html.
9. Huttenlocher, D. P., Klanderman, G. A. and Rucklidge, W. J. (1993) Comparing images using the Hausdorff distance. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 15, 850-863.
10. Jaeger, J., Surkova, S., Blagov, M., Janssens, H., Kosman, D., Kozlov, K. N., Manu, Myasnikova, E., Vanario-Alonso, C. E., Samsonova, M., Sharp, D. H. and Reinitz, J. (2004) Dynamic control of positional information in the early Drosophila embryo. Nature, 430, 368-371.
11. Kass, M., Witkin, A. and Terzopoulos, D. (1988) Snakes: Active contour models. International Journal of Computer Vision, 1, 321-331.
12. Kennedy, J. and Eberhart, R. (1995) Particle swarm optimization. Neural Networks, 1995. Proceedings, IEEE International Conference on, 4, 1942-1948.
13. Kim, H.-L. (2003) Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells. Experimental and Molecular Medicine, 35, 460-466.
14. Kumar, S., Jayaraman, K., Panchanathan, S., Gurunathan, R., Marti-Subirana, A. and Newfeld, S. J. (2002) BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics, 162, 2037-2047.
15. Lee, J.-Y., Colinas, J., Wang, J., Mace, D., Ohler, U. and Benfey, P. (2006) Transcriptional and post- transcriptional regulation of transcription factor expression in Arabidopsis roots. PNAS, 103, 6055-6060.
16. Luc, V. and Pierre, S. (1991) Watersheds in digital spaces: An efficient algorithm based on immersion simulations. IEEE Trans. Pattern Anal. Mach. Intell., 13, 583-598.
17. Maintz, J. B. A. and Viergever, M. A. (1998) A survey of medical image registration. Medical Image Analysis, 2, 1-36.
18. Ogniewicz, R. and Ilg, M. (1992) Voronoi skeletons: Theory and applications. In Proc. IEEE Conf. Computer Vision and Pattern Recognition, CVPR, pp. 63-69.
19. Park, P. J., Cao, Y. A., Lee, S. Y., Kim, J.-W., Chang, M. S., Hart, R. and Choi, S. (2004) Current issues for DNA microarrays: Platform comparison, double linear amplification, and universal RNA reference. Journal of Biotechnology, 112, 225-245.
20. Peng, H. and Myers, E. W. (2004) Comparing in situ mRNA expression patterns of Drosophila embryos. In 8th Conf. on Computational Molecular Biology (San Diego, CA, 2004), pp. 157-166.
21. Development Core Team (2005) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org. ISBN 3-900051-07-0.
22. Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S., Richards, S., Ashburner, M., Hartenstein, V., Celniker, S. and Rubin, G. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology, 3, research:0088.1-0088.14.
23. van Ruissen, F., Ruijter, J., Schaaf, G., Asgharnegad, L., Zwijnenburg, D., Kool, M. and Baas, F. (2005) Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix genechips. BMC Genomics, 6, 91.
24. Woods, R. P., Grafton, S. T., Holmes, C. J., Cherry, S. R. and Mazziotta, J. C. (1998) Automated Image Registration: I. general methods and intrasubject, intramodality validation. Journal of Computer Assisted Tomography, 22, 139-152.
25. Wu, J.-Q. and Pollard, T. D. (2005) Counting cytokinesis proteins globally and locally in fission Yeast. Science, 310, 310-314.
26. Zitova, B. and Flusser, J. (2003) Image registration methods: A survey. Image and Vision Computing, 21, 977-1000.