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

Dondrup M, Albaum S, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Kuester H, Linke B, Mertens D, Mittard-Runte V, et al. (2009)
BMC Bioinformatics 10(1): 50.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
URN
urn:nbn:de:0070-pub-16353214
Autor*in
Dondrup, Michael; Albaum, StefanUniBi ; Griebel, Thasso; Henckel, KoljaUniBi; Jünemann, SebastianUniBi; Kahlke, Tim; Kleindt, Christiane KatjaUniBi; Kuester, Helge; Linke, BurkhardUniBi; Mertens, Dominik; Mittard-Runte, VirginieUniBi; Neuweger, HeikoUniBi
Alle
Einrichtung
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
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.
Erscheinungsjahr
2009
Zeitschriftentitel
BMC Bioinformatics
Band
10
Ausgabe
1
Art.-Nr.
50
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1635321

Zitieren

Dondrup M, Albaum S, Griebel T, et al. EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics. 2009;10(1): 50.
Dondrup, M., Albaum, S., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., et al. (2009). EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics, 10(1), 50. https://doi.org/10.1186/1471-2105-10-50
Dondrup, Michael, Albaum, Stefan, Griebel, Thasso, Henckel, Kolja, Jünemann, Sebastian, Kahlke, Tim, Kleindt, Christiane Katja, et al. 2009. “EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data”. BMC Bioinformatics 10 (1): 50.
Dondrup, M., Albaum, S., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Kuester, H., Linke, B., Mertens, D., et al. (2009). EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10:50.
Dondrup, M., et al., 2009. EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics, 10(1): 50.
M. Dondrup, et al., “EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data”, BMC Bioinformatics, vol. 10, 2009, : 50.
Dondrup, M., Albaum, S., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C.K., Kuester, H., Linke, B., Mertens, D., Mittard-Runte, V., Neuweger, H., Runte, K.J., Tauch, A., Tille, F., Pühler, A., Goesmann, A.: EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics. 10, : 50 (2009).
Dondrup, Michael, Albaum, Stefan, Griebel, Thasso, Henckel, Kolja, Jünemann, Sebastian, Kahlke, Tim, Kleindt, Christiane Katja, Kuester, Helge, Linke, Burkhard, Mertens, Dominik, Mittard-Runte, Virginie, Neuweger, Heiko, Runte, Kai J., Tauch, Andreas, Tille, Felix, Pühler, Alfred, and Goesmann, Alexander. “EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data”. BMC Bioinformatics 10.1 (2009): 50.
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PMID: 17483229
The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum.
Brinkrolf K, Brune I, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17227685
Characterization of a carbohydrate transporter from symbiotic glomeromycotan fungi.
Schussler A, Martin H, Cohen D, Fitz M, Wipf D., Nature 444(7121), 2006
PMID: 17167486
Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza.
Hohnjec N, Vieweg MF, Puhler A, Becker A, Kuster H., Plant Physiol. 137(4), 2005
PMID: 15778460
Identification and expression regulation of symbiotically activated legume genes.
Kuster H, Vieweg MF, Manthey K, Baier MC, Hohnjec N, Perlick AM., Phytochemistry 68(1), 2006
PMID: 17081575
The Sequence Analysis and Management System – SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
Bekel T, Henckel K, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., 2009
MAGE Software Toolkit
AUTHOR UNKNOWN, 0
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
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