Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed.
The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures.
When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization.
Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.
Resource Type: Resource
Version: Latest Version
gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service
NSF, American Cancer Society, March of Dimes, Basil O'Connor Starter Scholar Research Award, DBI-0543017, RSG-06-179-01-MBC, 5-FY05-1224
Free, Acknowledgement requested
Organelle DB: A Database of Organelles and Protein Complexes
Additional Resource Types
database, d spatial image, image collection, data repository
human, mouse, plant, arabidopsis thaliana, drosophila melanogaster, caenorhabditis elegans, saccharomyces cerevisiae, other, eukaryota
Created 5 years ago by Anonymous
- Wiwatwattana N
- Nucleic Acids Res.
- 2007 4
Organelle DB (http://organelledb.lsi.umich.edu) is a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes. Since its release in 2004, Organelle DB has grown by 20% to encompass over 30,000 proteins from 138 eukaryotic organisms. Each protein in Organelle DB is presented with its subcellular localization, primary sequence and a detailed description of its function, as available. All records in Organelle DB have been annotated using controlled vocabulary from the Gene Ontology consortium. Protein localization data are inherently visual, and Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we report here the development of 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.
- Wiwatwattana N
- Nucleic Acids Res.
- 2005 1
To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.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. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu.