With the technologies and resources available today, it is prudent to make the most of our data by performing analyses across multiple-modalities and bringing those results together. Especially in cancer, it is particularly useful to perform full characterization by correlating structural variations with their functional consequences.
Our Nexus Copy Number software for years provided the ability to integrate sequence variants and gene expression results with copy number allowing identifications of genomic hotspots. A list of differentially expressed genes could be integrated as up and down values across the CNV profile of a set of samples. But now with Nexus Copy Number 8.0, gene expression results can be integrated on a per sample basis allowing a more in-depth and concise look at genomic changes and functional impacts.
Integration of gene expression results per sample allows creation of an expression profile for the set of samples within Nexus Copy Number showing the frequency of up or down regulated genes within different regions and also allows segregation of samples into subgroups within the entire cohort.
Frequency plot of gene expression results of the sample cohort at the top (red, down-regulated; blue, upregulated) and CNV profiles of individual samples below)
Learn more about integration of gene expression results in Nexus Copy Number 8.0 by attending our upcoming webinar on July 21:
In this webinar, Dr. Andrea O’Hara will perform integrated analysis using copy number, sequence variants, and RNA-Seq data from a TCGA kidney chromophobe (KICH) cohort. With a live software demo, she will
- present aggregate and concordance analysis to identify subgroups
- find statistically significant correlations between gene expression and CNV to identify potential driver genes of interest
- evaluate the overall impact of these changes on survival.
Integrated view of CNV probes, B-allele frequency, and gene expression probes plots for a single sample.