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.

Download
OA
Journal Article | Published | English
Author
Abstract
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.
Publishing Year
ISSN
PUB-ID

Cite this

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.
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.
Main File(s)
File Name
Access Level
OA Open Access
Last Uploaded
2016-02-08T13:52:10Z

This data publication is cited in the following publications:
This publication cites the following data publications:

24 Citations in Europe PMC

Data provided by Europe PubMed Central.

A stress-induced small RNA modulates alpha-rhizobial cell cycle progression.
Robledo M, Frage B, Wright PR, Becker A., PLoS Genet. 11(4), 2015
PMID: 25923724
Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells.
Wippermann A, Klausing S, Rupp O, Albaum SP, Buntemeyer H, Noll T, Hoffrogge R., Appl. Microbiol. Biotechnol. 98(2), 2014
PMID: 24146078
Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress.
Chi BK, Busche T, Van Laer K, Basell K, Becher D, Clermont L, Seibold GM, Persicke M, Kalinowski J, Messens J, Antelmann H., Antioxid. Redox Signal. 20(4), 2014
PMID: 23886307
Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas.
Schmidtke C, Abendroth U, Brock J, Serrania J, Becker A, Bonas U., PLoS Pathog. 9(9), 2013
PMID: 24068933
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.
Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J., BMC Genomics 14(), 2013
PMID: 23895370
Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates.
Fan B, Carvalhais LC, Becker A, Fedoseyenko D, von Wiren N, Borriss R., BMC Microbiol. 12(), 2012
PMID: 22720735
Arabitol metabolism of Corynebacterium glutamicum and its regulation by AtlR.
Laslo T, von Zaluskowski P, Gabris C, Lodd E, Ruckert C, Dangel P, Kalinowski J, Auchter M, Seibold G, Eikmanns BJ., J. Bacteriol. 194(5), 2012
PMID: 22178972
Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii.
Toepel J, Albaum SP, Arvidsson S, Goesmann A, la Russa M, Rogge K, Kruse O., BMC Genomics 12(), 2011
PMID: 22118351
Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.
Ryan RP, Vorholter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat. Rev. Microbiol. 9(5), 2011
PMID: 21478901
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis.
Lohse M, Nunes-Nesi A, Kruger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B., Plant Physiol. 153(2), 2010
PMID: 20388663
Mayday--integrative analytics for expression data.
Battke F, Symons S, Nieselt K., BMC Bioinformatics 11(), 2010
PMID: 20214778
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Albaum SP, Neuweger H, Franzel B, Lange S, Mertens D, Trotschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
TRUNCATULIX--a data warehouse for the legume community.
Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Kuster H, Goesmann A., BMC Plant Biol. 9(), 2009
PMID: 19210766

53 References

Data provided by Europe PubMed Central.

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

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 19200358
PubMed | Europe PMC

Search this title in

Google Scholar