EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Open Access
- 6 February 2009
- journal article
- research article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 10 (1) , 50
- https://doi.org/10.1186/1471-2105-10-50
Abstract
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.Keywords
This publication has 43 references indexed in Scilit:
- NCBI GEO: archive for high-throughput functional genomic dataNucleic Acids Research, 2009
- The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequencesMicrobiology, 2008
- CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome dataBMC Systems Biology, 2007
- The Extracytoplasmic Function-Type Sigma Factor SigM of Corynebacterium glutamicum ATCC 13032 Is Involved in Transcription of Disulfide Stress-Related GenesJournal of Bacteriology, 2007
- Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic contextBMC Bioinformatics, 2007
- The IclR-Type Transcriptional Repressor LtbR Regulates the Expression of Leucine and Tryptophan Biosynthesis Genes in the Amino Acid ProducerCorynebacterium glutamicumJournal of Bacteriology, 2007
- CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysisNucleic Acids Research, 2006
- Standardizing global gene expression analysis between laboratories and across platformsNature Methods, 2005
- Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray ExperimentsStatistical Applications in Genetics and Molecular Biology, 2004
- Significance analysis of microarrays applied to the ionizing radiation responseProceedings of the National Academy of Sciences, 2001