Mathematical characterization of three-dimensional gene expresssion patterns

L da F Costa; M S Barbosa; E T M Manoel; J Streicher; G B Müller

doi:10.1093/bioinformatics/bth135

Mathematical characterization of three-dimensional gene expresssion patterns

Titel in Übersetzung: Mathematische Charakterisierung von dreidimensionalen Genexpressionsmustern

L da F Costa
, M S Barbosa
, E T M Manoel
, J Streicher
, G B Müller

Publikation: Beitrag in Fachzeitschrift (peer-reviewed) › Artikel in Fachzeitschrift

9 Zitate (Scopus)

Abstract

Motivation: Die Bedeutung einer systematischen Methodik für die mathematische Charakterisierung von dreidimensionalen Genexpressionsmustern in der Embryonalentwicklung.
Methoden: Durch die Kombination von Lakunaritäts- und multiskaligen Fraktalitätsanalysen mit computergestützten Methoden der dreidimensionalen Rekonstruktion ist es möglich, neue Informationen aus in situ Hybridisierungsstudien zu gewinnen. Lakunarität und Fraktalität sind geeignete Maße für die wolkenartigen Genaktivierungssignale in embryonalen Geweben.

Titel in Übersetzung	Mathematische Charakterisierung von dreidimensionalen Genexpressionsmustern
Originalsprache	Englisch
Seiten (von - bis)	1653-1662
Seitenumfang	10
Fachzeitschrift	Bioinformatics
Jahrgang	20
Ausgabenummer	11
DOIs	https://doi.org/10.1093/bioinformatics/bth135
Publikationsstatus	Veröffentlicht - 22 Juli 2004
Extern publiziert	Ja

ASJC Scopus Sachgebiete

Computational Mathematics
Molekularbiologie
Biochemie
Statistik und Wahrscheinlichkeit
Angewandte Informatik
Theoretische Informatik und Mathematik

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title = "Mathematical characterization of three-dimensional gene expresssion patterns",

abstract = "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.",

keywords = "Animals, Culture Techniques, DNA-Binding Proteins/genetics, Embryo, Mammalian/metabolism, Fractals, Gene Expression Profiling/methods, Gene Expression Regulation/physiology, Image Interpretation, Computer-Assisted/methods, Imaging, Three-Dimensional/methods, In Situ Hybridization, Fluorescence/methods, Mice, Microscopy, Fluorescence/methods, Muscle Proteins/genetics, Myogenic Regulatory Factor 5, Numerical Analysis, Computer-Assisted, Pattern Recognition, Automated, Tissue Distribution, Trans-Activators/genetics, Transcriptional Activation",

author = "Costa, \{L da F\} and Barbosa, \{M S\} and Manoel, \{E T M\} and J Streicher and M{\"u}ller, \{G B\}",

note = "Funding Information: L.d.F.C is grateful to FAPESP (99/12765-2) and CNPq (468413/00-6 and 301422/92-3) for financial support. M.S.B is supported by FAPESP (02/02504-01). The left–right symmetry analysis was funded by HFSP grant to L.d.C and G.B.M.",

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doi = "10.1093/bioinformatics/bth135",

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AU - Costa, L da F

AU - Barbosa, M S

AU - Manoel, E T M

AU - Streicher, J

AU - Müller, G B

N1 - Funding Information: L.d.F.C is grateful to FAPESP (99/12765-2) and CNPq (468413/00-6 and 301422/92-3) for financial support. M.S.B is supported by FAPESP (02/02504-01). The left–right symmetry analysis was funded by HFSP grant to L.d.C and G.B.M.

PY - 2004/7/22

Y1 - 2004/7/22

N2 - 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.

AB - 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.

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KW - Imaging, Three-Dimensional/methods

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KW - Mice

KW - Microscopy, Fluorescence/methods

KW - Muscle Proteins/genetics

KW - Myogenic Regulatory Factor 5

KW - Numerical Analysis, Computer-Assisted

KW - Pattern Recognition, Automated

KW - Tissue Distribution

KW - Trans-Activators/genetics

KW - Transcriptional Activation

UR - https://www.scopus.com/pages/publications/4444261719

U2 - 10.1093/bioinformatics/bth135

DO - 10.1093/bioinformatics/bth135

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Mathematical characterization of three-dimensional gene expresssion patterns

Abstract

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