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TMAD specifications

Information


Unique identifier OMICS_21381
Name TMAD
Alternative name Stanford Tissue MicroArray Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Robert Marinelli

Publication for Stanford Tissue MicroArray Database

TMAD citations

 (4)
library_books

Recurrent rearrangements of the Myb/SANT like DNA binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma

2017
PLoS One
PMCID: 5315303
PMID: 28212443
DOI: 10.1371/journal.pone.0171265

[…] by immunohistochemistry using an anti-MSANTD3 antibody (LS-C146308, 1:2400 dilution; LifeSpan Biosciences) and peroxidase-based chromogenic staining (EnVision, Dako). All slides were uploaded to the Stanford Tissue Microarray Database []. Cores were evaluated for nuclear staining and assigned a score of strong (2), moderate (1), weak (+/-), negative (-), or uninterpretable/missing core (<100 eval […]

library_books

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

2016
PMCID: 4990152
PMID: 27538578
DOI: 10.1093/database/baw118

[…] atabases (MID); NLM HyperDoc Visible Human Project color, CAT and MRI image samples; The Histology Image Dataset (histologyDS); The Cancer Genome Atlas (TCGA); International Cancer Genome Consortium, Stanford Tissue Microarray Database (TMA); MITOS dataset, Cancer Image Database (caIMAGE); DPA’s Whole Slide Imaging Repository; Atlas of Bleast Histology; Histology Photo Album, Tissue Acquisition an […]

library_books

Application and evaluation of automated semantic annotation of gene expression experiments

2009
Bioinformatics
PMCID: 2687992
PMID: 19376825
DOI: 10.1093/bioinformatics/btp259

[…] mably for this reason, GenoText's results include many terms that are of limited use in information retrieval, such as ‘total’. Similar automated mapping for cancer terms has been demonstrated on the Stanford Tissue Microarray database (Shah et al., ). By manually evaluating a sample of annotations, they estimated 86% precision and 95% recall. Another system, ‘Whatizit’ provides a web-based system […]

library_books

Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions

2006
BMC Bioinformatics
PMCID: 1574358
PMID: 16889662
DOI: 10.1186/1471-2105-7-369

[…] ssed genes generally show a higher standard error than strongly-expressed genes (log-transformed data). As a consequence, the newly-defined μ- and MAD-test statistics, tμ = μ1 - μ2 = mean(s - s*) and tMAD = mean(|s - s*|), respectively. (s = log S, s* = log S*), do not contain the standard error. The μ-test, and also V&S, appeared to be almost unbiased with respect to expression strength. The MAD- […]

Citations

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TMAD institution(s)
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
TMAD funding source(s)
Supported by the Howard Hughes Medical Institute (HHMI) and a grant from the National Institutes of Health (5R01 CA77097).

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