2008
DOI: 10.1186/1471-2105-9-493
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EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

Abstract: Background: Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management.

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Cited by 13 publications
(15 citation statements)
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“…In databases like Oncomine, Flymine [13], Ingenuity, EMAAS [14], MiMiR [15] and many others around the world, microarray data can be imported, queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. However, none of these databases provide an analysis platform for absolute gene expression profiling.…”
Section: Discussionmentioning
confidence: 99%
“…In databases like Oncomine, Flymine [13], Ingenuity, EMAAS [14], MiMiR [15] and many others around the world, microarray data can be imported, queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. However, none of these databases provide an analysis platform for absolute gene expression profiling.…”
Section: Discussionmentioning
confidence: 99%
“…Visualisation of consensus regions together with gene representation allows the explorative assessment of the data. Another project is the Extensible MicroArray Analysis System (EMAAS) application created by Butcher and colleagues from Imperial College (UK) and the National Cancer Institute at Frederick (MD, USA) to provide simple, robust access to updated resources for microarray analysis [19]. When looking at specific gene information, their program generates an interactive expression profile plot and concomitantly brings forth the respective GeneCards information, thereby allowing further scrutiny of experimental data.…”
Section: Genecards Utilisation Examplesmentioning
confidence: 99%
“…The MiMiR middleware is used by EMAAS to securely access the appropriate experimental information, using Java Server Pages (JSPs) and Servlets. EMAAS is currently being used to perform data quality assessment, pre-processing, statistical analysis and functional enrichment analysis of Affymetrix 3' and Exon/Gene ST arrays, with scope to add further functionality for other platforms such as Illumina, Agilent and Codelink arrays [ 20 ].…”
Section: Construction and Contentmentioning
confidence: 99%
“…Here we describe new software components and enhancements of the original infrastructure that allow researchers to securely submit, access, share and analyse microarray and meta-data. Specifically, we have created: (i) a re-engineered hardware and software architecture that protects the MiMiR database integrity and enables secure online sharing of unpublished and public data amongst registered users; (ii) a new web based annotation tool allowing researchers to easily and quickly submit information about their experiments and samples; (iii) new sophisticated curation and annotation tools which automatically create annotated experiments in MiMiR and enable in-house annotators to check it and add ontology terms and systematic naming conventions; (iv) a clinical Data Mapping Tool to securely capture clinical information in a systematic way within an appropriate ethical framework; (v) a new user-friendly web interface that is used by researchers to visualise extensive experimental annotation, to download data and quality assessment reports and to share un-published datasets with collaborators or other registered users of the system; (vi) a re-engineered MAGE-ML pipeline for exporting experiments from MiMiR into the ArrayExpress repository or into the Rosetta Resolver package for data analysis; (vii) programmatic access to MiMiR from the new open source microarray data analysis software package EMAAS [ 20 ], allowing users to export selected data and associated meta-data for analysis.…”
Section: Introductionmentioning
confidence: 99%