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Mayday - integrative analytics for expression data

Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
BMC Bioinformatics (Impact Factor: 2.67). 03/2010; 11(1):121. DOI: 10.1186/1471-2105-11-121
Source: PubMed

ABSTRACT DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.
We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved.
We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org.

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Available from: Florian Battke, Aug 06, 2015
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    • "Differentially expressed genes were determined by setting fixed thresholds taking the background noise of the self-hybridization into account. MayDay (Battke et al., 2010) was used for analysis of expression patterns in individual datasets. Microarray data were deposited at Gene Expression Omnibus database, GEO ID: GSE35832. "
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    • "We included a new visualization to analyze distributions of genetic variations in more detail. Furthermore, we integrated Reveal into our visual analytics software Mayday (Battke et al., 2010), allowing for combined and highly interactive analyses of genotypic and expression data as well as meta-data (e.g. disease phenotype). "
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    • "GenomeRing is integrated into our visual analytics platform Mayday (Battke et al., 2010) as a visualization which can display data from multiple perspecies data sets. Using Mayday's facilities for data and meta-information management, we can for example add information about gene expression in the GenomeRing visualization. "
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