Benefits and Features
- Access both plug-ins (DAPfinder and DAPview) and the required BRB-ArrayTools for free
- Filter microarray data using
- Gene expression coefficient of variability (CV)
- Standard Deviation (SD) or Inter-Quartile Range (IQR) outlier detection
- Minimum sample size criteria
- Custom list of gene-gene pairs
- Other BRB-ArrrayTools filtering methods like minimum fold change, spot filters, etc.
- Evaluate pairwise gene-gene correlations using
- Pearson correlation
- Spearman rank correlation
- Kendall Tau rank correlation
- Mutual information
- Compare pairwise gene-gene correlations using
- Approximate Fisher’s Z test comparisons for Pearson, Spearman, or Kendall correlations
- Exact permutation test methods for all correlation types
- DAPfinder results are easily imported into Cytoscape to visualize the entire network
- Display individual differences in gene coexpression using DAPview
Overview
DAPfinder and DAPview are two novel plug-ins for BRB-ArrayTools that can be used to compare two coexpression networks constructed from microarray data. The DAPfinder tool re-constructs gene coexpression networks and identifies significant differences in pairwise gene-gene coexpression between two phenotypes. Each significant difference in gene-gene association is identified as a Differentially Associated Pair (DAP), which represents a significant change in the coexpression network between the two phenotypes. Several choices of filtering methods—gene-gene association metrics, statistical testing methods, and multiple comparison adjustments—are available to help users build and compare their networks. Network results from DAPfinder can be easily displayed in Cytoscape, while individual differences in pairwise gene coexpression can be visualized using DAPview.
Access
DAPfinder and DAPview are provided free of charge by the NIAID.
Background
The NIAID Office of Cyber Infrastructure and Computational Biology created DAPfinder and DAPview.