TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Yinhai Wang, Declan Kieran, Jaine Blayney, Darragh McArt, Kienan Savage, Dean Fennell, Jacqueline James, Manuel Salto-Tellez, Peter Hamilton

Research output: Contribution to conferencePaperpeer-review

Abstract

Background: Popular approaches in human tissue-based biomarker discovery include tissue microarrays (TMAs) and DNA Microarrays (DMAs) for protein and gene expression profiling respectively. The data generated by these analytic platforms, together with associated image, clinical and pathological data currently reside on widely different information platforms, making searching and cross-platform analysis difficult. Consequently, there is a strong need to develop a single coherent database capable of correlating all available data types.

Method: This study presents TMAX, a database system to facilitate biomarker discovery tasks. TMAX organises a variety of biomarker discovery-related data into the database. Both TMA and DMA experimental data are integrated in TMAX and connected through common DNA/protein biomarkers. Patient clinical data (including tissue pathological data), computer assisted tissue image and associated analytic data are also included in TMAX to enable the truly high throughput processing of ultra-large digital slides for both TMAs and whole slide tissue digital slides. A comprehensive web front-end was built with embedded XML parser software and predefined SQL queries to enable rapid data exchange in the form of standard XML files.

Results & Conclusion: TMAX represents one of the first attempts to integrate TMA data with public gene expression experiment data. Experiments suggest that TMAX is robust in managing large quantities of data from different sources (clinical, TMA, DMA and image analysis). Its web front-end is user friendly, easy to use, and most importantly allows the rapid and easy data exchange of biomarker discovery related data. In conclusion, TMAX is a robust biomarker discovery data repository and research tool, which opens up the opportunities for biomarker discovery and further integromics research.
Original languageEnglish
Publication statusPublished - 2012
Event1st Digital Pathology Application & Development Conference in China - Kunming, China
Duration: 21 Sep 201224 Sep 2012

Conference

Conference1st Digital Pathology Application & Development Conference in China
Country/TerritoryChina
CityKunming
Period21/09/201224/09/2012

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