Perspective abstract


Nature Biotechnology 25, 547 - 554 (2007)
Published online: 4 May 2007 | doi:10.1038/nbt1304

Towards zoomable multidimensional maps of the cell

Zhenjun Hu1,5, Joe Mellor1,4,5, Jie Wu1, Minoru Kanehisa2, Joshua M Stuart3 & Charles DeLisi1


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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  1. Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.
  2. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan.
  3. Department of Biomolecular Engineering, Mail Stop SOE2, University of California at Santa Cruz, Santa Cruz, California 95064, USA.
  4. Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
  5. These authors contributed equally to this work.

Correspondence to: Charles DeLisi1 e-mail: delisi@bu.edu



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