Article

A geometric database for gene expression data

Authors:

Gregor Eichele,

Christina Thaller,

James CarsonAuthors Info & Claims

SGP '03: Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing

Pages 166 - 176

Published: 23 June 2003 Publication History

Abstract

As the logical next step after sequencing the mouse genome, biologists have developed laboratory methods for rapidly determining where each of the 30K genes in the mouse genome is synthesizing protein. Applying these methods to the mouse brain, biologists are currently generating large numbers of 2D cross-sectional images that record the expression pattern for each gene in the mouse genome. In this paper, we describe the structure of a geometric database for the mouse brain that allows biologists to organize and search this gene expression data. The central component of this database is an atlas that explicitly partitions the mouse brain into key anatomical regions. This atlas is represented as a Catmull-Clark subdivision mesh with anatomical regions separated by a network of B-spline crease curves. New gene expression images are added to the database by deforming this atlas onto each image using techniques developed for fitting subdivision surfaces to scatter data. Due to this partitioning of the subdivision mesh, user queries comparing expression data between various genes can be restricted to anatomical regions without difficulty while the multi-resolution structure of the subdivision mesh allows these queries to be processed efficiently.

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Cited By

Agarwal NXu XGopi MBatra DBrown MNatarajan V(2016)Robust registration of Mouse brain slices with severe histological artifactsProceedings of the Tenth Indian Conference on Computer Vision, Graphics and Image Processing10.1145/3009977.3010053(1-8)Online publication date: 18-Dec-2016
https://dl.acm.org/doi/10.1145/3009977.3010053
Le YKurkure UParagios NJu TCarson JKakadiaris I(2012)Similarity-Based appearance-prior for fitting a subdivision mesh in gene expression imagesProceedings of the 15th international conference on Medical Image Computing and Computer-Assisted Intervention - Volume Part I10.1007/978-3-642-33415-3_71(577-584)Online publication date: 1-Oct-2012
https://dl.acm.org/doi/10.1007/978-3-642-33415-3_71
Ng LPathak SKuan CLau CDong HSodt ADang CAvants BYushkevich PGee JHaynor DLein EJones AHawrylycz M(2007)Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse BrainIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/tcbb.2007.10354:3(382-393)Online publication date: 1-Jul-2007
https://dl.acm.org/doi/10.1109/tcbb.2007.1035
Show More Cited By

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A geometric database for gene expression data

Index terms have been assigned to the content through auto-classification.

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Information & Contributors

Information

Published In

cover image ACM Other conferences

SGP '03: Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing

June 2003

277 pages

ISBN:1581136870

Conference Chairs:
Leif Kobbelt
Aachen University (RWTH)
,
Peter Schröder
Caltech
,
Hugues Hoppe
Microsoft Research

Sponsors

EUROGRAPHICS: The European Association for Computer Graphics

In-Cooperation

SIGGRAPH: ACM Special Interest Group on Computer Graphics and Interactive Techniques

Publisher

Eurographics Association

Goslar, Germany

Publication History

Published: 23 June 2003

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Conference

SGP03

Sponsor:

EUROGRAPHICS

SGP03: Symposium on Geometry Processing

June 23 - 25, 2003

Aachen, Germany

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Overall Acceptance Rate 64 of 240 submissions, 27%

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Cited By

Agarwal NXu XGopi MBatra DBrown MNatarajan V(2016)Robust registration of Mouse brain slices with severe histological artifactsProceedings of the Tenth Indian Conference on Computer Vision, Graphics and Image Processing10.1145/3009977.3010053(1-8)Online publication date: 18-Dec-2016
https://dl.acm.org/doi/10.1145/3009977.3010053
Le YKurkure UParagios NJu TCarson JKakadiaris I(2012)Similarity-Based appearance-prior for fitting a subdivision mesh in gene expression imagesProceedings of the 15th international conference on Medical Image Computing and Computer-Assisted Intervention - Volume Part I10.1007/978-3-642-33415-3_71(577-584)Online publication date: 1-Oct-2012
https://dl.acm.org/doi/10.1007/978-3-642-33415-3_71
Ng LPathak SKuan CLau CDong HSodt ADang CAvants BYushkevich PGee JHaynor DLein EJones AHawrylycz M(2007)Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse BrainIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/tcbb.2007.10354:3(382-393)Online publication date: 1-Jul-2007
https://dl.acm.org/doi/10.1109/tcbb.2007.1035
Schaefer SMcPhail TWarren JFinnegan JDorsey J(2006)Image deformation using moving least squaresACM SIGGRAPH 2006 Papers10.1145/1179352.1141920(533-540)Online publication date: 30-Jul-2006
https://dl.acm.org/doi/10.1145/1179352.1141920
Schaefer SMcPhail TWarren J(2006)Image deformation using moving least squaresACM Transactions on Graphics10.1145/1141911.114192025:3(533-540)Online publication date: 1-Jul-2006
https://dl.acm.org/doi/10.1145/1141911.1141920
Bello MJu TWarren JCarson JChiu WThaller CEichele GKakadiaris I(2005)Hybrid segmentation framework for tissue images containing gene expression dataProceedings of the 8th international conference on Medical Image Computing and Computer-Assisted Intervention - Volume Part I10.1007/11566465_32(254-261)Online publication date: 26-Oct-2005
https://dl.acm.org/doi/10.1007/11566465_32

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