The Stanford Microarray Database (SMD;; 1) is a web-based, research-oriented database for DNA microarray data. As of April 2005, SMD contained data for over 50,000 hybridizations, generated by over 1000 users. In addition, data for nearly 9000 hybridizations, including the data underlying over 200 published manuscripts, were freely available from SMD at that time, for public use without restriction.

Most researchers, educators, and students will find SMD useful as a repository of a very large quantity of publicly available data, together with analysis tools suitable for exploratory, unsupervised analysis and discovery. At the time of this writing, most of the data available to the public were generated from two-color assays on printed cDNA microarrays (2). However, some data from experiments using Affymetrix GeneChips™ (single-channel data from high-density photolithographic arrays) are also available. SMD also has prepublication

From: Methods in Molecular Biology, vol. 338: Gene Mapping, Discovery, and Expression: Methods and Protocols Edited by: M. Bina © Humana Press Inc., Totowa, NJ

data from Agilent, NimbleGen, and CombiMatrix platforms, so it is likely that data from those platforms will eventually be made public.

This chapter concentrates primarily on the tools for browsing, selecting, downloading, and analyzing these public data.

Providing a vehicle for disseminating the results of published microarray data is only a secondary function of SMD. SMD was primarily designed and is used as a research-oriented database for ongoing, prepublication experiments. Registered users have access to tools to deposit data, annotate them to full compliance with the MIAME standards (3), share them with collaborators, and perform certain analyses that are too resource intensive for general public use. These functions are also briefly covered in this chapter, since most are of interest to any researcher conducting experiments or data analysis utilizing microarray data.

Additionally, there are many tools available to the database curators, for entering array designs, maintaining and updating annotations for genes, managing user accounts, and so forth; these will not be discussed here.

SMD may be found at SMD's source code and database schema are also available for local installation, under the MIT license (, at http://smd.stanford. edu/download/.

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