Abstract
Background: We previously introduced a method based on post hoc pairwise comparisons to analyze gene expression responses. This method utilized directed graphs to represent gene response to all treatment pairs. It has been found useful in identifying structure-activity relationships among drugs and differentiating genes sharing similar functional pathways. Directed graphs are descriptive, visually expressive and can benefit subsequent functional analysis. Results: mDAG is a web-based software package based on this established method for the analysis, visualization, and interpretation of patterns of responses in gene expression data involving multiple treatments. Genes with the same directed graph patterns hypothetically share similar biological function, which may be further analyzed using external tools. To facilitate subsequent functional analysis, several well-known tools have been incorporated into mDAG to help users explore hypotheses about gene function and regulation. This tool is useful for any studies that analyze comparatively response patterns in gene expression data with multiple treatments (chemicals, cell types, etc.). Availability: The (server/personal/demo) software is freely available at http://cetus.cs. memphis.edu/mdag.
Highlights
In gene expression studies with many treatments (e.g.[1,2]), it is desirable to employ a post hoc approach in which only k groups of gene expression values are k k 1measured and tests are made to compare how a gene responds to all pairs of treatments
We previously introduced a method based on post hoc pairwise comparisons to analyze gene expression responses
Results: mDAG is a web-based software package based on this established method for the analysis, visualization, and interpretation of patterns of responses in gene expression data involving multiple treatments
Summary
In gene expression studies with many treatments (e.g.[1,2]), it is desirable to employ a post hoc approach in which only k groups of gene expression values are k k 1measured and tests are made to compare how a gene responds to all pairs of treatments. Recent studies exploited directed graphs to represent patterns of gene response to all treatment pairs, such as [5,6]. We previously introduced a method based on post hoc pairwise comparisons to analyze gene expression responses This method utilized directed graphs to represent gene response to all treatment pairs. Results: mDAG is a web-based software package based on this established method for the analysis, visualization, and interpretation of patterns of responses in gene expression data involving multiple treatments. To facilitate subsequent functional analysis, several well-known tools have been incorporated into mDAG to help users explore hypotheses about gene function and regulation This tool is useful for any studies that analyze comparatively response patterns in gene expression data with multiple treatments (chemicals, cell types, etc.). Availability: The (server/personal/demo) software is freely available at http://cetus.cs. memphis.edu/mdag
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