Mathematical characterization of three-dimensional gene expression patterns

Author(s)

Costa, L. da F. ; Barbosa, M. S. ^[2] ; Manoel, E. T. M. ; Streicher, J. ; Müller, G. B.

• Document type: Journal article
• Source: Bioinformatics; v. 20, n. 11, p. 1653-1662, Jul. 2004.
• Field of knowledge: Physical Sciences and Mathematics - Computer Science

Abstract

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

• FAPESP's process: 02/02504-1 - Dynamic shape analysis
• Grantee: Marconi Soares Barbosa
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 99/12765-2 - Development and assessment of novel and accurate methods in shape analysis and computer vision
• Grantee: Luciano da Fontoura Costa
• Support Opportunities: Research Projects - Thematic Grants