Navigating public microarray databases

Penkett, Christopher J.; Bähler, Jürg

doi:10.1002/cfg.427

Cited by 8 publications

(6 citation statements)

References 47 publications

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“…The Society also set the standard data exchange format, known as the Microarray Genetic Expression Markup Language (MAGE-ML). Thorough reviews of the numerous databases in existence have been set out in the literature ( 31 ).…”

Section: Principles Of Transcriptome Analysismentioning

confidence: 99%

Emergent Transcriptomic Technologies and Their Role in the Discovery of Biomarkers of Liver Transplant Tolerance

2015

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Liver transplantation offers a unique window into transplant immunology due, in part, to the considerable proportion of recipients who develop immunological tolerance to their allograft. Biomarkers are able to identify and predict such a state of tolerance, and thereby able to establish suitable candidates for the minimization of hazardous immunosuppressive therapies, are not only of great potential clinical benefit but might also shed light on the immunological mechanisms underlying tolerance and rejection. Here, we review the emergent transcriptomic technologies serving as drivers of biomarker discovery, we appraise efforts to identify a molecular signature of liver allograft tolerance, and we consider the implications of this work on the mechanistic understanding of immunological tolerance.

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Section: Principles Of Transcriptome Analysismentioning

confidence: 99%

Emergent Transcriptomic Technologies and Their Role in the Discovery of Biomarkers of Liver Transplant Tolerance

2015

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“…, 2004). This need is being met by the large numbers of commercial and public DNA microarray database structures now available (Penkett and Bahler, 2004). Such repositories, for instance ArrayExpress (Brazma et al.…”

Section: Introductionmentioning

confidence: 99%

UPSC‐BASE –Populus transcriptomics online

et al. 2006

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SummaryThe increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purposedesigned storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

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“…A huge amount of data obtained through microarray technologies analyzed as described above are maintained in two ways [47]: (a) using a software, usually installed locally, that allows storage, querying and analysis of data captured on-site, and (b) databases that act as repositories for publicly available data, in particular, published data. Three important elements to be considered for sharing microarray data are i) a data annotation standard ii) a common data exchange format, and iii) public repositories analogous to DDBJ/EMBL/GenBank.…”

Section: Microarray Databasesmentioning

confidence: 99%

“…[ 54] scope of this article to review all the software and database repositories for microarray technologies, which have been thoroughly reviewed elsewhere [47].…”

Section: Consensusclustermentioning

confidence: 99%