ArticleBMC bioinformatics2007
TAMEE: data management and analysis for tissue microarrays.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Gene Expression Detection Assay for Cancer Clinical Use.Journal of Cancer · 2018Review
- PATMA: parser of archival tissue microarray.PeerJ · 2016Article
- TMA Navigator: Network inference, patient stratification and survival analysis with tissue microarray data.Nucleic acids research · 2013Article
- Extending the tissue microarray data exchange specification for inclusion of data analysis results.Journal of pathology informatics · 2011Article
- The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides.Journal of pathology informatics · 2011Article
- Using XML to encode TMA DES metadata.Journal of pathology informatics · 2011Article
- Article
- Datamining approach for automation of diagnosis of breast cancer in immunohistochemically stained tissue microarray images.The open medical informatics journal · 2010Article
- The Stanford Tissue Microarray Database.Nucleic acids research · 2008Article
- ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.Journal of the American Medical Informatics Association : JAMIAArticle
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories.
resultsTAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator.
conclusionWe have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from http://genome.tugraz.at/Software/TAMEE.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.