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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Mathematical characterization of three-dimensional gene expression patterns

L. da F. Costa 1,*, M. S. Barbosa 1, E. T. M. Manoel 1, J. Streicher 2 and G. B. Müller 3,4

1 Cybernetic Vision Research Group, GII-IFSC, Universidade de São Paulo, São Carlos, SP, Caixa Postal 369, 13560-970, Brasil, 2 Department of Anatomy and 3 Department of Zoology, Integrative Morphology Group, University of Vienna, 1090 Vienna, Austria and 4 Konrad Lorenz Institute for evolution and Cognition Research, 3422 Altenberg, Austria

Received on July 31, 2003; revised on December 18, 2003; accepted on December 19, 2004
Advance Access Publication February 26, 2004

Motivation: The importance of a systematic methodology for the mathematical characterization of three-dimensional gene expression patterns in embryonic development.

Methods: By combining lacunarity and multiscale fractal dimension analyses with computer-based methods of three-dimensional reconstruction, it becomes possible to extract new information from in situ hybridization studies. Lacunarity and fractality are appropriate measures for the cloud-like gene activation signals in embryonic tissues. The newly introduced multiscale method provides a natural extension of the fractal dimension concept, being capable of characterizing the fractality of geometrical patterns in terms of spatial scale. This tool can be systematically applied to three-dimensional patterns of gene expression.

Results: Applications are illustrated using the three-dimensional expression patterns of the myogenic marker gene Myf5 in a series of differentiating somites of a mouse embryo.

Contact: luciano{at}if.sc.usp.br

* To whom correspondence should be addressed.


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