Extraction of Differential Gene Expression
EDGE is a software package for the significance analysis of DNA microarray experiments
____ for both standard and time course experiments ____
based on our new Optimal Discovery Procedure and Time Course Methodology
Software based on the following articles...
- Storey JD. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing. Journal of the Royal Statistical Society, Series B, 69: 347-368. [PDF] [Web Site]
- Storey JD, Dai JY, and Leek JT. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics, 8: 414-432. [PDF] [Web Site] [Supp Info]
- Leek JT, Monsen EC, Dabney AR, and Storey JD. (2006) EDGE: Extraction and analysis of differential gene expression. Bioinformatics, 22: 507-508. [PDF]
- Storey JD, Xiao W, Leek JT, Tompkins RG, and Davis RW. (2005) Significance analysis of time course microarray experiments. Proceedings of the National Academy of Sciences, 102: 12837-12842. [PDF] [Web Site]
Significance analysis features...
- Software based on statistical theory developed in the Storey Lab
- Implements the new Optimal Discovery Procedure (ODP) -- click here for an explanation
- Performs significance analysis of regular "snapshot" experiments
- Performs significance analysis of time course experiments -- click here for an explanation
- Identifies genes differentially expressed across distinct biological groups or with respect to a continuous variable
- Accurately tests for over/under-expression and fold-change -- coming soon
- Self-contained gene expression analysis software -- open-source and free
- A fully point-and-click interface -- click here for some screen shots
- Data transformation and visualization
- Missing data imputation
- Principal components analysis (i.e., eigen-gene/eigen-array analysis)
- Automatic internet based queries of user chosen genes
Software by Jeffrey Leek, Alan Dabney, Eva Monsen and John Storey.