Abstract
BackgroundRegulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular conditions. The data derived out of microarray experiments is highly dimensional and often noisy, and interpretation of the results can get intricate. Although programs for the statistical analysis of microarray data exist, most of them lack an integration of analysis results and biological interpretation.ResultsWe have developed GEPAT, Genome Expression Pathway Analysis Tool, offering an analysis of gene expression data under genomic, proteomic and metabolic context. We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip. GEPAT imports various types of oligonucleotide and cDNA array data formats. Different normalization methods can be applied to the data, afterwards data annotation is performed. After import, GEPAT offers various statistical data analysis methods, as hierarchical, k-means and PCA clustering, a linear model based t-test or chromosomal profile comparison. The results of the analysis can be interpreted by enrichment of biological terms, pathway analysis or interaction networks. Different biological databases are included, to give various information for each probe on the chip. GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis. GEPAT relies on established data analysis packages, offers a modular approach for an easy extension, and can be run on a computer grid to allow a large number of users. It is freely available under the LGPL open source license for academic and commercial users at .ConclusionGEPAT is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data. An installation available for academic users can be found at .
Highlights
Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages
As we were unhappy with the separation of analysis and interpretation, we developed our own tool, GEPAT
Microarray experiments generate a large amount of data in a very short time
Summary
Microarray experiments generate a large amount of data in a very short time. In most cases it is not desirable to work with all these data at once. The dataset is shown in an overview table, giving annotation information for the spots and showing the gene expression values for the samples. An interpretation can be performed on any subset of data This integration is a major focus of GEPAT and distinguishes it from many other available tools for the analysis of gene expression data. The available pathways provide key information of the functional and metabolic systems within a living cell We use this database and color differential gene expression of the current working set onto a pathway, allowing the exploration of functional relationships between genes. Data handling functions serve as a framework that can be extended with various modules for data import, data analysis, data interpretation, subset selection and gene information. Tooltips are provided for each gene, allowing a quick detail investigation at interesting points of the genome, as shown in figure 4d
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