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Organelle DB


NAR Molecular Biology Database Collection entry number 713
Wiwatwattana N., Landau C., Cope G.J., Harp G., and Kumar A.
Department of Molecular, Cellular, and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
Contact anujk@umich.edu

Database Description

Organelle DB is a Web-accessible database cataloging proteins localized to a known organelle, subcellular structures, or protein complex in organisms throughout the eukaryotic kingdom. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, and M. musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results and actual fluorescent images from ongoing large-scale studies of protein localization in Saccharomyces cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium.

Recent Developments

Since its release in 2004, Organelle DB has grown by 20% to encompass over 30,000 proteins from 138 eukaryotic organisms. Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we have recently developed Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually “fun” interface. Organelle View can be accessed from the Organelle DB home page or directly at http://organelleview.lsi.umich.edu.

Acknowledgements

Organelle DB is supported by grant no. DBI 0543017 from the National Science Foundation.

References

1. Wiwatwattana, N. and Kumar, A. (2005) Organelle DB: a cross-species database of protein localization and function. Nucleic Acids Res. 33: D598-D604.


Go to the abstract in the NAR 2007 Database Issue.
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