Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views
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, 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: (i) gene
expression patterns defined by the spatial locations of cells expressing a
gene, and (ii) relationships between the expression levels of multiple genes.
PointCloudXplore provides users with two corresponding classes of data views:
(i) Physical Views based on the spatial relationships of cells in the embryo,
and (ii) 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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Gunther H. Weber, Oliber Rubel, Min-Yu Huang, Angela H. DePace, Charless C. Fowlkes, Soile V. E. Keranen, Cris L. Luengo Hendriks, Hans Hagen, David W. Knowles, Jitendra Malik, Mark D. Biggin, and Bernd Hamann. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE Transactions on Computational Biology and Bioinformatics, 6(2):296–309, 2009.BibTeX Reference
@article{Weber_TCBB_2008,author = "Weber, Gunther H. and Rubel, Oliber and Huang, Min-Yu and DePace, Angela H. and Fowlkes, Charless C. and Keranen, Soile V. E. and Hendriks, Cris L. Luengo and Hagen, Hans and Knowles, David W. and Malik, Jitendra and Biggin, Mark D. and Hamann, Bernd",
title = "Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views",
journal = "IEEE Transactions on Computational Biology and Bioinformatics",
year = "2009",
volume = "6(2)",
pages = "296-309",
tag = "biological_images"
}