External Data Integration Module
Integrating different modalities allows for a more comprehensive analysis of a project. The external data module does that by integrating miRNA, mRNA, and methylation results with copy number and allelic events to identify genomic “hot spots” of change. It shows the overlapping areas of changes (between gene expression results and copy number changes, for example) that are unlikely to happen by chance alone and provides easy access to associated genes, and functions in such regions.
Sample aberration frequency plot, top panel, and tracks of external gene lists, for gene expression, on the bottom (blue tick marks indicate significantly up-regulated genes, magenta tick marks, significantly down-regulated).
Features
- P-value statistics on significance of observed genes appearing in the same region as CNV or allelic events
- Interactive graphical display stacking copy number events, allelic events, and up/down regulated genes (or methylated regions) along with annotation tracks.
- Report table listing statistics and p-values correlating external data results with CNV and allelic events
- Report table listing regions, medians, p-value, and Q-bound
- Ability to perform GO term enrichment with a single click to discover affected functions
- Ability to add affected region as an annotation column to the samples table for further analysis
Applications
If other types of results (gene expression/methylation) are available for a project then this can be integrated with the copy number and allelic event changes within Nexus Copy Number to show correlation between these two types of analyses.
