Nexus Copy Number

Group samples based on aberration profiles using K-means or hierarchical clustering displaying a dendrogram with the ability to adjust the number of clusters and label clusters with sample attributes. Identify Gene Ontology (GO) terms enriched over the entire genome using GSEA or find GO terms significantly over represented in selected regions only.  Use the concordance function to identify genomic alterations co-occurring with copy number changes, LOH regions, or small mutations, and depict these relationships in a circular (Circos-like) plot.

Find statistically significant differences in genomic changes between biologically important subgroups using one of several different comparison types available (e.g. paired, sequential).  Results can be viewed in table format as well as in interactive graphical displays.  Easily view frequency plots of the subgroups in parallel along with indicators displaying those regions that are significantly different.

Nexus Copy Number was designed for scientists with robust statistical functions and rich interactive graphics.  It is a powerful desktop (Windows or Mac OS) solution allowing visualization and analysis of tens of thousands of high-density arrays in parallel.  Numerous statistical tools allow flexibility and ease in large cohort analyses as well as individual sample analysis and visualization with no bioinformatics or programming experience.

External data such as gene expression results and sequence variants can be loaded into the software allowing more complete analysis by integration of multiple modalities.  Sequence variants from MAF or VCF file allow analysis of point mutations, indels, inversions, etc. independently as well as integrated with copy number changes. Differentially regulated gene lists (results from expression arrays or RNA-seq) along with significance and fold change can be integrated on a per sample basis to identify genes with coordinating changes in gene expression and copy number or allelic events.

Nexus Copy Number software is bundled with the Nexus DB genomic data repository allowing querying of similar aberrations across thousands of samples from GEO, TCGA and more.  Search for keywords to find similar projects or samples with specific annotations.  You can share data and collaborate with colleagues using a secure data sharing scheme. Add the TCGA Premier product allowing access to high quality and manually curated data from TCGA for deeper studies involving survival analysis or tumor sub-type profiling.

Associate an unlimited number of sample annotations/attributes for further downstream analyses.  Use the predictive power tool to find correlations between continuous value attributes and genomic changes, perform survival analysis for cancer samples (with Kaplan-Meir plots), or stratify samples based on aberration profiles and phenotypes to identify driver mutations or identify therapeutic targets.