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Stanford Microarray Database


NAR Molecular Biology Database Collection entry number 22
Ball, C.A.1, Demeter, J.1, Gollub, G.1, Hebert, J.M.2, Hernandez-Boussard, T.1, Jin, H.1, Nitzberg, M.1, Wymore, F.1, Brown, P.O.1,3, Sherlock, G.4
1Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
2 Stanford Functional Genomics Facility, Center For Clinical Sciences Research, 269 Campus Drive, Room 4256 Stanford University, CA 94305-5163, USA
3Howard Hughes Medical Institute, Dept. of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
4Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305-5120, USA.

Database Description

The Stanford Microarray Database (SMD; http://smd.stanford.edu/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code, and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 5000 microarrays, including data from 130 publications, and this total is increasing rapidly. SMD makes use of many public sources of biological annotation, which are used to connect the entities on the microarrays with their most current biological information. This is of paramount importance, as expression data in the absence of biological context are meaningless.

Recent Developments

SMD has now adopted the MIAME standard, allowing researchers to annotate the experiments in a MIAME compliant fashion. Furthermore, SMD also enables the production of MAGE-ml for a user's experiments, which can be submitted to the ArrayExpress repository, which is increasingly becoming a requirement for publication.


Go to the abstract in the NAR 2007 Database Issue.
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