BioGRID: a general repository for interaction datasets - PubMed (original) (raw)

BioGRID: a general repository for interaction datasets

Chris Stark et al. Nucleic Acids Res. 2006.

Abstract

Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

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Figures

Figure 1

A sample search and result page provided by the BioGRID for the query yeast gene KSS1. Annotated results are collapsed to remove redundancy and hyperlinked to allow recursive searches and access to external resources. Graphical representation at upper left shows all interactions annotated with color-coded GO terms and experimental evidence. Graphs are generated by Osprey and may be downloaded in JPEG, PNG and SVG formats.

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References

1. 1. Pawson T., Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 2003;300:445–452. - PubMed
2. 1. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature. 1999;402:C47–C52. - PubMed
3. 1. Bader G.D., Heilbut A., Andrews B., Tyers M., Hughes T., Boone C. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol. 2003;13:344–356. - PubMed
4. 1. Bader G.D., Hogue C.W. Analyzing yeast protein–protein interaction data obtained from different sources. Nat. Biotechnol. 2002;20:991–997. - PubMed
5. 1. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., Bork P. Comparative assessment of large-scale data sets of protein–protein interactions. Nature. 2002;417:399–403. - PubMed

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