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SOURCE


NAR Molecular Biology Database Collection entry number 358
Diehn, M.1, Sherlock, G.2, Binkley, G.2, Jin, H.2, Hernandez-Boussard, T.2, Cherry, J.M.2, Brown, P.O.3, Alizadeh, A.A.4
1Department of Biochemistry, Stanford University School of Medicine Stanford, CA 94305
2Department of Genetics, Stanford University School of Medicine Stanford, CA 94305
3Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine Stanford, CA 94305
4Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143

Database Description

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE’s GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCE’s batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at http://smd.stanford.edu/cgi-bin/source/sourceSearch.

Recent Developments

Ongoing curation of publicly available microarray gene expression datasets, currently totaling more than 4 million measurements.

Acknowledgements

We wish to thank members of the Stanford Microarray Database and the Brown and Botstein laboratories for helpful discussions and advice. This work was supported by N.I.H. grant CA85129-04 (P.O.B.) and National Institute of General Medical Sciences training grant GM07365 (A.A.A., M.D.). P.O.B. is an associate investigator of the Howard Hughes Medical Institute.

References

Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. (2003). SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31: 219-223.


Go to the abstract in the NAR 2003 Database Issue.
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