EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data

被引：53

作者：

Dondrup, Michael ^{[1
]}

Albaum, Stefan P.

Griebel, Thasso ^{[2
]}

Henckel, Kolja ^{[1
]}

Juenemann, Sebastian

Kahlke, Tim ^{[3
]}

Kleindt, Christiane K. ^{[1
,4
]}

Kuester, Helge ^{[6
]}

Linke, Burkhard

Mertens, Dominik

Mittard-Runte, Virginie

Neuweger, Heiko ^{[1
]}

Runte, Kai J.

Tauch, Andreas ^{[4
]}

Tille, Felix

Puehler, Alfred ^{[4
,5
]}

Goesmann, Alexander

机构：

[1] Univ Bielefeld, Ctr Biotechnol, Int NRW Grad Sch Bioinformat & Genome Res, D-33594 Bielefeld, Germany

[2] Univ Jena, Lehrstuhl Bioinformat, D-07743 Jena, Germany

[3] Univ Tromso, Fac Med, Dept Mol Biotechnol, Inst Med Biol, N-9037 Tromso, Norway

[4] Univ Bielefeld, Inst Genome Res & Syst Biol, D-33594 Bielefeld, Germany

[5] Univ Bielefeld, Fac Biol, D-33594 Bielefeld, Germany

[6] Leibniz Univ Hannover, Inst Plant Genet, Unit Plant Genom 4, D-30419 Hannover, Germany

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

关键词：

GENE-EXPRESSION DATA; CORYNEBACTERIUM-GLUTAMICUM; REGULATORY NETWORK; TRANSCRIPTOME; PLATFORM; IDENTIFICATION; NORMALIZATION; BIOCONDUCTOR; ONTOLOGY; STORAGE;

D O I：

10.1186/1471-2105-10-50

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

引用

页数：14