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Towards zoomable multidimensional maps of the cell

Nature Biotechnology volume 25, pages 547–554 (2007)Cite this article

Abstract

The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. Visualization is a vital aid in integrating and interpreting such data. We describe emerging approaches for representing and visualizing systems data and for achieving semantic zooming, or changes in information density concordant with scale. A central challenge is to move beyond the display of a static network to visualizations of networks as a function of time, space and cell state, which capture the adaptability of the cell. We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes.

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Figure 1: Comparison of different graphical representations of a portion of the cell cycle's START-related events at G1 phase in Saccharomyces cerevisiae.
Figure 2: A metagraph of the network of protein complexes discovered through tandem affinity mass spectrometry tagging by Gavin et al. and grouped and colored to indicate subsequent functional assignments59.
Figure 3: A network using the same set of complexes as Figure 2, except with edges representing interactions derived by large-scale two-hybrid assays55.
Figure 4: Model representing the same data as Figure 1, represented by a metagraph showing transitions between views.
Figure 5: Using a metagraph to integrate two annotation methods.
Figure 6: A zoomable map of metabolic modules.
Figure 7: Illustration of steps to determine a network in Homo sapiens using the metagraph concept, where each metanode represents a set of orthologous eukaryotic genes from the COG database53.

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Author notes

  1. Joe Mellor

    Present address: Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,

  2. Zhenjun Hu and Joe Mellor: These authors contributed equally to this work.

Authors and Affiliations

  1. Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, 02215, Massachusetts, USA

    Zhenjun Hu, Joe Mellor, Jie Wu & Charles DeLisi

  2. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan

    Minoru Kanehisa

  3. Department of Biomolecular Engineering, Mail Stop SOE2, University of California at Santa Cruz, Santa Cruz, 95064, California, USA

    Joshua M Stuart

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Correspondence to Charles DeLisi.

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Hu, Z., Mellor, J., Wu, J. et al. Towards zoomable multidimensional maps of the cell. Nat Biotechnol 25, 547–554 (2007). https://doi.org/10.1038/nbt1304

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