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The Stanford Tissue Microarray Database.

Robert J Marinelli1, Kelli Montgomery, Chih Long Liu

  • 1Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA. bobm@stanford.edu

Nucleic Acids Research
|November 9, 2007
PubMed
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The Stanford Tissue Microarray Database (TMAD) provides public access to annotated tissue images and expression data. Researchers worldwide utilize TMAD for analyzing tissue microarrays, advancing cancer research and image analysis.

Area of Science:

  • Biomedical Informatics
  • Pathology
  • Genomics

Background:

  • Tissue microarrays (TMAs) enable high-throughput analysis of protein and transcript abundance in hundreds of tissue cores simultaneously.
  • Immunohistochemistry (IHC) and in situ hybridization (ISH) are key techniques for detecting protein and nucleic acid levels, respectively.
  • Publicly accessible databases are crucial for data sharing and reproducibility in biomedical research.

Purpose of the Study:

  • To describe the Stanford Tissue Microarray Database (TMAD) as a public resource.
  • To highlight TMAD's utility for pathologists and researchers in designing, viewing, scoring, and analyzing TMAs.
  • To facilitate image processing research by providing access to annotated images and scores.

Main Methods:

  • TMAD archives multi-wavelength fluorescence and bright-field images of TMAs.

Related Experiment Videos

  • Data includes annotated tissue images and associated expression data.
  • The NCI Thesaurus ontology is integrated for cancer-related tissue searching.

    • Main Results:

    • As of July 2007, TMAD contained 205,161 images from 1488 TMA slides, archiving 349 probes.
    • 31,306 images for 68 probes on 125 slides were publicly released.
    • 12 publications have utilized the publicly available TMAD data.

    Conclusions:

    • TMAD serves as a valuable public resource for TMA data dissemination and analysis.
    • The database supports diverse research applications, including cancer research and the development of image classification algorithms.
    • TMAD promotes collaborative research and data sharing within the scientific community.