Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views
Gunther Weber, Oliber Rubel, Min-Yu Huang, Angela DePace, Charless Fowlkes, Soile Keranen, Cris Hendriks, Hans Hagen, David Knowles, Jitendra Malik, Mark Biggin, Bernd Hamann
icon 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

    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"