Literature DB >> 14651856

EMMA: a platform for consistent storage and efficient analysis of microarray data.

Michael Dondrup1, Alexander Goesmann, Daniela Bartels, Jörn Kalinowski, Lutz Krause, Burkhard Linke, Oliver Rupp, Alexander Sczyrba, Alfred Pühler, Folker Meyer.   

Abstract

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).

Mesh:

Year:  2003        PMID: 14651856     DOI: 10.1016/j.jbiotec.2003.08.010

Source DB:  PubMed          Journal:  J Biotechnol        ISSN: 0168-1656            Impact factor:   3.307


  43 in total

1.  Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011.

Authors:  E Krol; A Becker
Journal:  Mol Genet Genomics       Date:  2004-06-23       Impact factor: 3.291

2.  Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program.

Authors:  Fikri El Yahyaoui; Helge Küster; Besma Ben Amor; Natalija Hohnjec; Alfred Pühler; Anke Becker; Jérôme Gouzy; Tatiana Vernié; Clare Gough; Andreas Niebel; Laurence Godiard; Pascal Gamas
Journal:  Plant Physiol       Date:  2004-10-01       Impact factor: 8.340

3.  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.

Authors:  Natalija Hohnjec; Martin F Vieweg; Alfred Pühler; Anke Becker; Helge Küster
Journal:  Plant Physiol       Date:  2005-03-18       Impact factor: 8.340

4.  The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula.

Authors:  Verena Tellström; Björn Usadel; Oliver Thimm; Mark Stitt; Helge Küster; Karsten Niehaus
Journal:  Plant Physiol       Date:  2007-01-12       Impact factor: 8.340

5.  Metabolic and transcriptomic phenotyping of inorganic carbon acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942.

Authors:  Doreen Schwarz; Anke Nodop; Jan Hüge; Stephanie Purfürst; Karl Forchhammer; Klaus-Peter Michel; Hermann Bauwe; Joachim Kopka; Martin Hagemann
Journal:  Plant Physiol       Date:  2011-01-31       Impact factor: 8.340

6.  EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods.

Authors:  Christian Firnhaber; Alfred Pühler; Helge Küster
Journal:  Planta       Date:  2005-06-21       Impact factor: 4.116

7.  The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.

Authors:  Iris Brune; Nina Jochmann; Karina Brinkrolf; Andrea T Hüser; Robert Gerstmeir; Bernhard J Eikmanns; Jörn Kalinowski; Alfred Pühler; Andreas Tauch
Journal:  J Bacteriol       Date:  2007-01-26       Impact factor: 3.490

8.  Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.

Authors:  Jan Baumbach; Andreas Tauch; Sven Rahmann
Journal:  Brief Bioinform       Date:  2008-12-12       Impact factor: 11.622

9.  The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti.

Authors:  Francesco Pini; Benjamin Frage; Lorenzo Ferri; Nicole J De Nisco; Saswat S Mohapatra; Lucilla Taddei; Antonella Fioravanti; Frederique Dewitte; Marco Galardini; Matteo Brilli; Vincent Villeret; Marco Bazzicalupo; Alessio Mengoni; Graham C Walker; Anke Becker; Emanuele G Biondi
Journal:  Mol Microbiol       Date:  2013-08-19       Impact factor: 3.501

10.  ADP-glucose pyrophosphorylase-deficient pea embryos reveal specific transcriptional and metabolic changes of carbon-nitrogen metabolism and stress responses.

Authors:  Kathleen Weigelt; Helge Küster; Twan Rutten; Aaron Fait; Alisdair R Fernie; Otto Miersch; Claus Wasternack; R J Neil Emery; Christine Desel; Felicia Hosein; Martin Müller; Isolde Saalbach; Hans Weber
Journal:  Plant Physiol       Date:  2008-11-05       Impact factor: 8.340

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