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

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

Research output: Journal article (peer-reviewed) › Journal article

9 Citations (Scopus)

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.

Translated title of the contribution	Mathematische Charakterisierung von dreidimensionalen Genexpressionsmustern
Original language	English
Pages (from-to)	1653-1662
Number of pages	10
Journal	Bioinformatics
Volume	20
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/bth135
Publication status	Published - 22 Jul 2004
Externally published	Yes

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

ASJC Scopus subject areas

Computational Mathematics
Molecular Biology
Biochemistry
Statistics and Probability
Computer Science Applications
Computational Theory and Mathematics

Access to Document

10.1093/bioinformatics/bth135

Cite this

@article{0f9e8b1024b64e6e80ec68e2af523a92,

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.",

year = "2004",

month = jul,

day = "22",

doi = "10.1093/bioinformatics/bth135",

language = "English",

volume = "20",

pages = "1653--1662",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "11",

}

TY - JOUR

T1 - Mathematical characterization of three-dimensional gene expresssion patterns

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.

KW - Animals

KW - Culture Techniques

KW - DNA-Binding Proteins/genetics

KW - Embryo, Mammalian/metabolism

KW - Fractals

KW - Gene Expression Profiling/methods

KW - Gene Expression Regulation/physiology

KW - Image Interpretation, Computer-Assisted/methods

KW - Imaging, Three-Dimensional/methods

KW - In Situ Hybridization, Fluorescence/methods

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 - http://www.scopus.com/inward/record.url?scp=4444261719&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bth135

DO - 10.1093/bioinformatics/bth135

M3 - Journal article

C2 - 14988120

SN - 1367-4803

VL - 20

SP - 1653

EP - 1662

JO - Bioinformatics

JF - Bioinformatics

IS - 11

ER -

Mathematical characterization of three-dimensional gene expresssion patterns

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this