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

Dondrup, Michael; Albaum, Stefan P.; Griebel, Thasso; Henckel, Kolja; Jünemann, Sebastian; Kahlke, Tim; Kleindt, Christiane Katja; Küster, H.; Linke, Burkhard; Mertens, Dominik; Mittard-Runte, Virginie; Neuweger, Heiko; Runte, Kai J.; Tauch, Andreas; Tille, Felix; Pühler, Alfred; Goesmann, Alexander

doi:10.1186/1471-2105-10-50

Cited by 66 publications

(56 citation statements)

References 45 publications

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“…To minimize the number of false-positive signals, the data were stringently filtered to obtain genes with at least six statistically significant values out of eight technical replicates present on the two microarrays along with an error probability of less than 5% for the Student t test. Normalization of the hybridization data by the Lowess function and t test statistics was accomplished by use of the EMMA 2.2 software package (25,26). Genes with a statistical significance of a P value of Յ0.05, a changed transcript abundance of Ϯ2 (M Ն 1 or M Յ Ϫ1), and a minimal signal intensity of an A value of Ն9 (negative controls) were regarded as differentially expressed.…”

Section: Methodsmentioning

confidence: 99%

Arabitol Metabolism of Corynebacterium glutamicum and Its Regulation by AtlR

Laslo

Zaluskowski

Gabris

et al. 2011

Journal of Bacteriology

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Expression profiling of Corynebacterium glutamicum in comparison to a derivative deficient in the transcriptional regulator AtlR (previously known as SucR or MtlR) revealed eight genes showing more than 4-fold higher mRNA levels in the mutant. Four of these genes are located in the direct vicinity of the atlR gene, i.e., xylB, rbtT, mtlD, and sixA, annotated as encoding xylulokinase, the ribitol transporter, mannitol 2-dehydrogenase, and phosphohistidine phosphatase, respectively. Transcriptional analysis indicated that atlR and the four genes are organized as atlR-xylB and rbtT-mtlD-sixA operons. Growth experiments with C. glutamicum and C. glutamicum ⌬atlR, ⌬xylB, ⌬rbtT, ⌬mtlD, and ⌬sixA derivatives with sugar alcohols revealed that (

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Section: Methodsmentioning

confidence: 99%

Arabitol Metabolism of Corynebacterium glutamicum and Its Regulation by AtlR

Laslo

Zaluskowski

Gabris

et al. 2011

Journal of Bacteriology

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“…However, there are conflicts between the aims of designing unique probes for all genes including those with sequence similarities and the necessity of obtaining oligonucleotides with physical properties useful for hybridization procedures. Unfavourable trade-offs in these fields are often unavoidable [129]. The underlying drawbacks of microarray design have been reduced by technological progress but not fundamentally eliminated, despite advancements in design and data analysis.…”

Section: Validation and Augmentation Of Genome Annotations Based On Tmentioning

confidence: 99%

“…Despite being a stand-alone application, it is able to communicate with the well-established genome annotation software GenDB (c) [77], which can be complemented with SAMS for the analysis of shorter DNA sequence data [269]. Specialized tools facilitate the genome-based interpretation of microarray-based transcriptome data (d; EMMA; [129]), proteome data (e; QuPE; [172]), and gas chromatography-mass spectrometry (GC-MS)-based metabolome data (f; MeltDB; [181]). Recently, in addition, the ALLocator software (g) became available for liquid chromatography (LC)-MS-based metabolite analyses [184], as well as applications for enhanced data visualization (h; ProMeTra; [172]) and for the automated generation of metabolic networks in Systems Biology Markup Language (SBML) format (i; CARMEN; [199]).…”

Section: Genomic Basicsmentioning

confidence: 99%

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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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“…Normalization and t-statistics were carried out using the EMMA2.8.2 microarray data analysis software developed at the Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University [66]. Genes were classified as differentially expressed with P <0.05 and M >1 or M <À1 (at least a twofold difference).…”

Section: Analysis Of Sam Levelsmentioning

confidence: 99%

RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti

Baumgardt

Melior²,

Madhugiri

et al. 2017

Microbiology

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The ribonucleases (RNases) E and J play major roles in E. coli and Bacillus subtilis, respectively, and co-exist in Sinorhizobium meliloti. We analysed S. meliloti 2011 mutants with mini-Tn5 insertions in the corresponding genes rne and rnj and found many overlapping effects. We observed similar changes in mRNA levels, including lower mRNA levels of the motility and chemotaxis related genes flaA, flgB and cheR and higher levels of ndvA (important for glucan export). The acyl-homoserine lactone (AHL) levels were also higher during exponential growth in both RNase mutants, despite no increase in the expression of the sinI AHL synthase gene. Furthermore, several RNAs from both mutants migrated aberrantly in denaturing gels at 300 V but not under stronger denaturing conditions at 1300 V. The similarities between the two mutants could be explained by increased levels of the key methyl donor S-adenosylmethionine (SAM), since this may result in faster AHL synthesis leading to higher AHL accumulation as well as in uncontrolled methylation of macromolecules including RNA, which may strengthen RNA secondary structures. Indeed, we found that in both mutants the N 6 -methyladenosine content was increased almost threefold and the SAM level was increased at least sevenfold. Complementation by induced ectopic expression of the respective RNase restored the AHL and SAM levels in each of the mutants. In summary, our data show that both RNase E and RNase J are needed for SAM homeostasis in S. meliloti.

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

Cited by 66 publications

References 45 publications

Arabitol Metabolism of Corynebacterium glutamicum and Its Regulation by AtlR

Arabitol Metabolism of Corynebacterium glutamicum and Its Regulation by AtlR

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti

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