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Database Commons - TMAD

TMAD

Citations: 55

z-index 3.30

Short name TMAD
Full name The Stanford Tissue Microarray Database
Description TMAD is a public resource for disseminating annotated tissue images and associated expression data.
URL https://tma.im/cgi-bin/home.pl
Year founded 2008
Last update & version     
Availability Free to all users
University/Institution hosted Howard Hughes Medical Institute
Address Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA
City Stanford
Province/State CA
Country/Region United States
Contact name Robert J. Marinelli
Contact email bobm@stanford.edu
Data type(s)
Major organism(s)
Keyword(s)
  • Microarray
Publication(s)
  • The Stanford Tissue Microarray Database. [PMID: 17989087]

    Robert J Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H Shah, Wijan Prapong, Michael Nitzberg, Zachariah K Zachariah, Gavin J Sherlock, Yasodha Natkunam, Robert B West, Matt van de Rijn, Patrick O Brown, Catherine A Ball
    Nucleic acids research 2008:36(Database issue)
    55 Citations (Google Scholar as of 2016-03-01)

    Abstract: 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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Tags

Expression
Microarray

Record metadata

  • Created on: 2015-07-28
  • Curated by:
    • Mengwei Li [2016-02-16]
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