BPS Expression Plot

Create BPS Expression plot based on expression P-values and save as PDF

Expression plots illustrate the degree of up- or down-regulation of genes in the vicinity of an integration event (or any region of interest). Disregulation for a given sample (case) is relative to a population of control samples, and is expressed as P-values (or false discovery rate, FDR). Smaller P-values indicate a higher degree of disregulation. Expression data can come from precalculated TCGA RSEM dataset, or calculated from RNA-Seq data directly (RPKM). Plots of both datasets are shown below.

Expression Plot Key

Expression plots provide a compact visual representation of gene position, size, name, and strand information, together with degree of disregulation relative to controls. Larger "bubbles" indicate more disregulation, with blue and red indicating down- and up-regulation, respectively.

TCGA-BA-4077-01 expression: RPKM Analysis

Virus integration occurs in gene RAD51B, and exons upstream and downstream are treated independently (resulting in two RAD51B "genes"). We find significant upregulation of RAD51B exons downstream of the integration event.

TCGA-BA-4077-01 expression: RSEM Analysis

Analysis of TCGA RSEM data yields similar results as the RPKM analysis.