ArticleBMC bioinformatics2009
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis.Cancers · 2019Article
- An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.Frontiers in microbiology · 2018Article
- The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.BMC genomics · 2017Article
- AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Overexpression of the primary sigma factor geneMetabolic engineering communications · 2017Article
- Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation.Nucleic acids research · 2017Article
- Systems Biology to Support Nanomaterial Grouping.Advances in experimental medicine and biology · 2017Review
- Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis inFrontiers in microbiology · 2017Article
- New SigD-regulated genes identified in the rhizobacterium Bacillus amyloliquefaciens FZB42.Biology open · 2016Article
- A stress-induced small RNA modulates alpha-rhizobial cell cycle progression.PLoS genetics · 2015Article
- Exploring the role of sigma factor gene expression on production by Corynebacterium glutamicum: sigma factor H and FMN as example.Frontiers in microbiology · 2015Article
- Systems toxicology: from basic research to risk assessment.Chemical research in toxicology · 2014Article
- Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress.Antioxidants & redox signaling · 2014Article
- Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells.Applied microbiology and biotechnology · 2014Article
- A novel type of N-acetylglutamate synthase is involved in the first step of arginine biosynthesis in Corynebacterium glutamicum.BMC genomics · 2013Article
- Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas.PLoS pathogens · 2013Article
- Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.BMC genomics · 2013Article
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17 authors.
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Abstract
backgroundUnderstanding 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.
resultsThe 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.
conclusionOur 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.
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