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Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views
April-June 2009 (vol. 6 no. 2)
pp. 1-1
ASCII Text
x 
 
G.H. Weber, O. Rubel, A.H. DePace, C.C. Fowlkes, S.V.E. Keranen, C.L. Luengo Hendriks, H. Hagen, D.W. Knowles, J. Malik, M.D. Biggin, B. Hamann, "Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 1-1, April-June, 2009.
 
 
BibTex
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@article{ 10.1109/TCBB.2007.70249,
author = {G.H. Weber and O. Rubel and A.H. DePace and C.C. Fowlkes and S.V.E. Keranen and C.L. Luengo Hendriks and H. Hagen and D.W. Knowles and J. Malik and M.D. Biggin and B. Hamann},
title = {Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {6},
number = {2},
issn = {1545-5963},
year = {2009},
pages = {1-1},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.70249},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views
IS - 2
SN - 1545-5963
SP1
EP1
EPD - 1-1
A1 - G.H. Weber,
A1 - O. Rubel,
A1 - A.H. DePace,
A1 - C.C. Fowlkes,
A1 - S.V.E. Keranen,
A1 - C.L. Luengo Hendriks,
A1 - H. Hagen,
A1 - D.W. Knowles,
A1 - J. Malik,
A1 - M.D. Biggin,
A1 - B. Hamann,
PY - 2009
KW - genetics
KW - bioinformatics
KW - cellular biophysics
KW - embryo cells
KW - three-dimensional gene expression
KW - visual exploration
KW - gene regulatory networks
KW - Drosophila embryos
KW - PointCloudXplore
KW - visualization tool
KW - Gene expression
KW - Embryo
KW - Data visualization
KW - Computer science
KW - Animals
KW - Computer networks
KW - Spatial resolution
KW - Bioinformatics
KW - Biology computing
KW - Cellular networks
KW - scatter plots.
KW - Interactive data exploration
KW - three-dimensional gene expression
KW - spatial expression patterns
KW - information visualization
KW - visualization
KW - physical views
KW - multiple linked views
KW - brushing
KW - Picture/Image Generation
KW - General
VL - 6
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
G.H. Weber, Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
O. Rubel, Dept. of Comput. Sci., Univ. of Kaiserslautern, Kaiserslautern, Germany
A.H. DePace, Med. Sch., Dept. of Syst. Biol., Harvard Univ., Boston, MA, USA
C.C. Fowlkes, Dept. of Comput. Sci., Univ. of California, Irvine, CA, USA
S.V.E. Keranen, Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
C.L. Luengo Hendriks, Centre for Image Anal., Uppsala Univ., Uppsala, Sweden
H. Hagen, Dept. of Comput. Sci., Univ. of Kaiserslautern, Kaiserslautern, Germany
D.W. Knowles, Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
J. Malik, Comput. Sci. Div., Univ. of California, Berkeley, CA, USA
M.D. Biggin, Lawrence Berkeley Nat. Lab., Berkeley, CA, USA
B. Hamann, Dept. of Comput. Sci., Univ. of California, Davis, CA, USA
During animal development, complex patterns of gene expression provide positional information within the embryo. To better understand the underlying gene regulatory networks, the Berkeley Drosophila Transcription Network Project (BDTNP) has developed methods that support quantitative computational analysis of three-dimensional (3D) gene expression in early Drosophila embryos at cellular resolution. We introduce PointCloudXplore (PCX), an interactive visualization tool that supports visual exploration of relationships between different genes' expression using a combination of established visualization techniques. Two aspects of gene expression are of particular interest: 1) gene expression patterns defined by the spatial locations of cells expressing a gene and 2) relationships between the expression levels of multiple genes. PCX provides users with two corresponding classes of data views: 1) physical views based on the spatial relationships of cells in the embryo and 2) abstract views that discard spatial information and plot expression levels of multiple genes with respect to each other. Cell selectors highlight data associated with subsets of embryo cells within a View. Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses.

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Index Terms:
genetics,bioinformatics,cellular biophysics,embryo cells,three-dimensional gene expression,visual exploration,gene regulatory networks,Drosophila embryos,PointCloudXplore,visualization tool,Gene expression,Embryo,Data visualization,Computer science,Animals,Computer networks,Spatial resolution,Bioinformatics,Biology computing,Cellular networks,scatter plots.,Interactive data exploration,three-dimensional gene expression,spatial expression patterns,information visualization,visualization,physical views,multiple linked views,brushing,Picture/Image Generation,General
Citation:
G.H. Weber, O. Rubel, A.H. DePace, C.C. Fowlkes, S.V.E. Keranen, C.L. Luengo Hendriks, H. Hagen, D.W. Knowles, J. Malik, M.D. Biggin, B. Hamann, "Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 1-1, April-June 2009, doi:10.1109/TCBB.2007.70249
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