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Nucleic Acids Research Advance Access originally published online on November 7, 2007
Nucleic Acids Research 2008 36(Database issue):D871-D877; doi:10.1093/nar/gkm861
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Nucleic Acids Research, 2008, Vol. 36, Database issue D871-D877
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

The Stanford Tissue Microarray Database

Robert J. Marinelli1,2,*, Kelli Montgomery3, Chih Long Liu4, Nigam H. Shah4, Wijan Prapong4, Michael Nitzberg1, Zachariah K. Zachariah1, Gavin J. Sherlock5, Yasodha Natkunam3, Robert B. West3, Matt van de Rijn3, Patrick O. Brown1,2 and Catherine A. Ball1

1Department of Biochemistry, Stanford University School of Medicine, 2Howard Hughes Medical Institute, 3Department of Pathology, Stanford University School of Medicine, 4Department of Medicine, Stanford University and 5Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

*To whom correspondence should be addressed. Tel: +1 650 723 6719; Fax: +1 650 725 7811; Email: bobm{at}stanford.edu

Received August 9, 2007. Revised September 27, 2007. Accepted September 27, 2007.

The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license.


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