EMMA: a platform for consistent storage and efficient analysis of microarray data
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 135-146.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Dondrup, M.;
Goesmann, AlexanderUniBi 
;
Bartels, D.;
Kalinowski, JörnUniBi;
Krause, L.;
Linke, BurkhardUniBi;
Rupp, O.;
Sczyrba, AlexanderUniBi ;
Pühler, AlfredUniBi ;
Meyer, F.
;
Bartels, D.;
Kalinowski, JörnUniBi;
Krause, L.;
Linke, BurkhardUniBi;
Rupp, O.;
Sczyrba, AlexanderUniBi ;
Pühler, AlfredUniBi ;
Meyer, F.Einrichtung
Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Fakultät für Biologie
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Fakultät für Biologie
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Abstract / Bemerkung
As a high throughput technique, microarray experiments produce large data sets, consisting of measured data, laboratory protocols, and experimental settings. We have implemented the open source platform EMMA to store and analyze these data. The system provides automated pipelines for data processing and has a modular architecture that can be easily extended. EMMA features detailed reports about spots and their corresponding measurements. In addition to routine data analysis algorithms, the system can be integrated with other components that contain additional data sources (e.g. genome annotation systems). (C) 2003 Elsevier B.V. All rights reserved.
Stichworte
transcriptomics;
microarrays;
gene expression analysis;
data integration
Erscheinungsjahr
2003
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
106
Ausgabe
2-3
Seite(n)
135-146
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1609260
Zitieren
Dondrup M, Goesmann A, Bartels D, et al. EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY. 2003;106(2-3):135-146.
Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., et al. (2003). EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 135-146. https://doi.org/10.1016/j.jbiotec.2003.08.010
Dondrup, M., Goesmann, Alexander, Bartels, D., Kalinowski, Jörn, Krause, L., Linke, Burkhard, Rupp, O., Sczyrba, Alexander, Pühler, Alfred, and Meyer, F. 2003. “EMMA: a platform for consistent storage and efficient analysis of microarray data”. JOURNAL OF BIOTECHNOLOGY 106 (2-3): 135-146.
Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., Sczyrba, A., Pühler, A., and Meyer, F. (2003). EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY 106, 135-146.
Dondrup, M., et al., 2003. EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY, 106(2-3), p 135-146.
M. Dondrup, et al., “EMMA: a platform for consistent storage and efficient analysis of microarray data”, JOURNAL OF BIOTECHNOLOGY, vol. 106, 2003, pp. 135-146.
Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., Sczyrba, A., Pühler, A., Meyer, F.: EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY. 106, 135-146 (2003).
Dondrup, M., Goesmann, Alexander, Bartels, D., Kalinowski, Jörn, Krause, L., Linke, Burkhard, Rupp, O., Sczyrba, Alexander, Pühler, Alfred, and Meyer, F. “EMMA: a platform for consistent storage and efficient analysis of microarray data”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 135-146.
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The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula.
Tellström V, Usadel B, Thimm O, Stitt M, Küster H, Niehaus K., Plant Physiol 143(2), 2007
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The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.
Brune I, Jochmann N, Brinkrolf K, Hüser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Pühler A, Tauch A., J Bacteriol 189(7), 2007
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The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes.
Nakunst D, Larisch C, Hüser AT, Tauch A, Pühler A, Kalinowski J., J Bacteriol 189(13), 2007
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FarR, a putative regulator of amino acid metabolism in Corynebacterium glutamicum.
Hänssler E, Müller T, Jessberger N, Völzke A, Plassmeier J, Kalinowski J, Krämer R, Burkovski A., Appl Microbiol Biotechnol 76(3), 2007
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Suppression of the pathogen-inducible Medicago truncatula putative protease-inhibitor MtTi2 does not influence root infection by Aphanomyces euteiches but results in transcriptional changes from wildtype roots
Nyamsuren O, Firnhaber C, Hohnjec N, Becker A, Küster H, Krajinski F., Plant Sci 173(2), 2007
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A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues.
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CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
Baumbach J., BMC Bioinformatics 8(), 2007
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The DeoR-type transcriptional regulator SugR acts as a repressor for genes encoding the phosphoenolpyruvate:sugar phosphotransferase system (PTS) in Corynebacterium glutamicum.
Gaigalat L, Schlüter JP, Hartmann M, Mormann S, Tauch A, Pühler A, Kalinowski J., BMC Mol Biol 8(), 2007
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CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
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Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
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Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula.
Hohnjec N, Henckel K, Bekel T, Gouzy J, Dondrup M, Goesmann A, Kuster H., Functional plant biology : FPB. 33(8), 2006
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Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression.
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Transcriptome profiling reveals the importance of plasmid pSymB for osmoadaptation of Sinorhizobium meliloti.
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The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032.
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EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods.
Firnhaber C, Pühler A, Küster H., Planta 222(2), 2005
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Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res 33(web server issue), 2005
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DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum.
Silberbach M, Hüser A, Kalinowski J, Pühler A, Walter B, Krämer R, Burkovski A., J Biotechnol 119(4), 2005
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Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation.
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The Sinorhizobium meliloti fur gene regulates, with dependence on Mn(II), transcription of the sitABCD operon, encoding a metal-type transporter.
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Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011.
Krol E, Becker A., Mol Genet Genomics 272(1), 2004
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Krol E, Becker A., Mol Genet Genomics 272(1), 2004
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Wide-range transcriptional modulating effect of ntrR under microaerobiosis in Sinorhizobium meliloti.
Puskás LG, Nagy ZB, Kelemen JZ, Rüberg S, Bodogai M, Becker A, Dusha I., Mol Genet Genomics 272(3), 2004
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Puskás LG, Nagy ZB, Kelemen JZ, Rüberg S, Bodogai M, Becker A, Dusha I., Mol Genet Genomics 272(3), 2004
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Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program.
El Yahyaoui F, Küster H, Ben Amor B, Hohnjec N, Pühler A, Becker A, Gouzy J, Vernié T, Gough C, Niebel A, Godiard L, Gamas P., Plant Physiol 136(2), 2004
PMID: 15466239
El Yahyaoui F, Küster H, Ben Amor B, Hohnjec N, Pühler A, Becker A, Gouzy J, Vernié T, Gough C, Niebel A, Godiard L, Gamas P., Plant Physiol 136(2), 2004
PMID: 15466239
Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses.
Manthey K, Krajinski F, Hohnjec N, Firnhaber C, Pühler A, Perlick AM, Küster H., Mol Plant Microbe Interact 17(10), 2004
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Manthey K, Krajinski F, Hohnjec N, Firnhaber C, Pühler A, Perlick AM, Küster H., Mol Plant Microbe Interact 17(10), 2004
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Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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