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. 2005 Jan 1;33(Database issue):D580-2.
doi: 10.1093/nar/gki006.

The Stanford Microarray Database accommodates additional microarray platforms and data formats

Catherine A Ball  1 , Ihab A B Awad, Janos Demeter, Jeremy Gollub, Joan M Hebert, Tina Hernandez-Boussard, Heng Jin, John C Matese, Michael Nitzberg, Farrell Wymore, Zachariah K Zachariah, Patrick O Brown, Gavin Sherlock
Affiliations

The Stanford Microarray Database accommodates additional microarray platforms and data formats

Catherine A Ball et al. Nucleic Acids Res. .

Abstract

The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.

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Figures

Figure 1
Figure 1
Screenshot of SMD's Microarray Data Repository. The repository allows the users to store their data sets created within SMD, upload datasets from other sources, share them with colleagues and collaborators and jump off to a variety of data retrieval, selection, transformation and analysis options. The interface provides the option to view any other repository for which a user has permission to view data. SMD users can store datasets before and after filtering and centering in pre-clustering (.pcl) files. Using repository options, a user can view, download, cluster and filter data, delete data from the repository, edit descriptions and permissions for a data set, perform singular value decomposition and collapse the data based on human genes into UniGene clusters, sections of chromosome or other ‘synthetic genes’ constructed by the researcher. Clustered data can also be stored, and users have additional options to view a heat-map cluster using GeneXplorer (8) to view spot-image clusters displaying or to view both heat-map and spot-image clusters side by side.
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