Abstract

BackgroundDNA 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.ResultsWe 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.ConclusionsWe 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.

Highlights

  • DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics

  • During a normal microarray experiment, several of these methods have to be used in combination

  • A custom-designed Affymetrix array containing 22,779 probe sets interrogating genes, intergenic regions, and predicted noncoding RNAs was used to study the gene expression in mostly hourly intervals starting at 20 h after inoculation, up to 60 h [23]

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Summary

Introduction

DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. 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. Since their inception in the early 1990s, DNA microarrays have revolutionized many areas of biological research. They are a fast and relatively inexpensive tool used for genome-wide studies of gene expression, epigenetic modifications, binding sites of DNA-binding proteins, copy-number variation as well as for resequencing projects. Such a framework must allow the quick addition of new methods and support their development via rapid prototyping

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