Dataset Information

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.

ABSTRACT: BACKGROUND: High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously. The utility of a plot, in turn, is contingent on both its interpretability and its efficiency. RESULTS: The shivplot, a graphical technique motivated by microarrays but applicable to any replicated high-throughput data set, is described. The plot capitalizes on the strengths of three well-established plotting graphics--a boxplot, a distribution density plot, and a variability vs intensity plot--by effectively combining them into a single representation. CONCLUSION: The utility of the new display is illustrated with microarray data sets. The proposed graph, retaining all the information of its precursors, conserves space and minimizes redundancy, but also highlights features of the data that would be difficult to appreciate from the individual display components. We recommend the use of the shivplot both for exploratory data analysis and for the communication of experimental data in publications.

SUBMITTER: Woody OZ

PROVIDER: S-EPMC1679802 | biostudies-other | 2006

REPOSITORIES: biostudies-other

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The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.

Woody Owen Z OZ Nadon Robert R

Source code for biology and medicine 20061108

<h4>Background</h4>High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously. The utility of a plot, in turn, is contingent on both its interpretability and its efficiency.<h4>Results</h4>The shivplot, a ...[more]

PMID: 17147786

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Project description:BACKGROUND: In the past decade, the field of molecular biology has become increasingly quantitative; rapid development of new technologies enables researchers to investigate and address fundamental issues quickly and in an efficient manner which were once impossible. Among these technologies, DNA microarray provides methodology for many applications such as gene discovery, diseases diagnosis, drug development and toxicological research and it has been used increasingly since it first emerged. Multiple tools have been developed to interpret the high-throughput data produced by microarrays. However, many times, less consideration has been given to the fact that an extensive and effective interpretation requires close interplay between the bioinformaticians who analyze the data and the biologists who generate it. To bridge this gap and to simplify the usability of such tools we developed Eureka-DMA - an easy-to-operate graphical user interface that allows bioinformaticians and bench-biologists alike to initiate analyses as well as to investigate the data produced by DNA microarrays. RESULTS: In this paper, we describe Eureka-DMA, a user-friendly software that comprises a set of methods for the interpretation of gene expression arrays. Eureka-DMA includes methods for the identification of genes with differential expression between conditions; it searches for enriched pathways and gene ontology terms and combines them with other relevant features. It thus enables the full understanding of the data for following testing as well as generating new hypotheses. Here we show two analyses, demonstrating examples of how Eureka-DMA can be used and its capability to produce relevant and reliable results. CONCLUSIONS: We have integrated several elementary expression analysis tools to provide a unified interface for their implementation. Eureka-DMA's simple graphical user interface provides effective and efficient framework in which the investigator has the full set of tools for the visualization and interpretation of the data with the option of exporting the analysis results for later use in other platforms. Eureka-DMA is freely available for academic users and can be downloaded at http://blue-meduza.org/Eureka-DMA.

Dataset Information

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.

Publications

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.

Similar Datasets

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