MicroMetal: Microarray Meta-Analysis

DNA microarrays enable high-throughput gathering of gene expression data with greater ease than ever before. Recently, with the commitment of funding agencies such as NIH to require research groups to publish experimental data on the Internet, the next challenge has become to develop appropriate data analysis tools that take advantage of the vast quantities of data available.

Many of the current software tools for bioinformatics research are inadequate to support the typical research process for three main reasons: (1) life scientists find the cost of the learning curve associated with some tools outweighs the benefits attainable from their use; (2) current tools do not guide users through entire hypothesis testing procedures; and (3) current tools typically only allow the user to utilize a very narrow scope of experimental evidence at any one time (e.g., a set of samples from a single experiment).

The aim of this thesis is to address these issues in the design and development of a new investigatory software tool. Being conscious of the research process, a primary aim of the design is to guide the user through complete hypothesis testing procedures. User interaction with the software centers around a wizard-style interface that organizes the elements of a well defined research process into a logical step-by-step procedure. This concept drastically reduces the learning curve of the tool. Furthermore, great importance has been placed on the user.s ability to easily access and efficiently utilize publicly available experimental data, so that knowledge can be inferred from a variety of sources simultaneously. When working with large numbers of microarray datasets, it is natural to provide methods for analyzing the datasets. metadata. Such an overview will greatly enhance the user.s understanding of the data by showing contrasts, consistent traits, anomalies and so on, between the datasets being used in an investigation.

These concepts have been applied to the implementation of an initial investigatory procedure. The workflow aims to explore the conditions under which two genes of interest in a particular species behave similarly. One application of such an investigation is to discover the characteristics of known metabolic pathway relationships between genes.