Epiviz: interactive visual analytics for functional genomics data

Abstract

Visualization is an integral aspect of genomics data analysis. Algorithmic-statistical analysis and interactive visualization are most effective when used iteratively. Epiviz (http://epiviz.cbcb.umd.edu/), a web-based genome browser, and the Epivizr Bioconductor package allow interactive, extensible and reproducible visualization within a state-of-the-art data-analysis platform.

Figure 1

Colon cancer methylome visualization using Epiviz. Long regions of methylation changes in colon cancer (Hypo- and Hyper-methylation blocks) are shown along with the smoothed base-pair resolution data (Methylation Colon Cancer and Normal) used to define them. Colon gene expression data on an MA plot (top right) shows genes within the viewing region that are differentially expressed. Data from the gene expression barcode shows transcriptome state across multiple tissues (top left). Highlighted region shows the brushing feature linking all charts by spatial location. This workspace can be accessed at http://epiviz.cbcb.umd.edu/?ws=cDx4eNK96Ws.

Figure 2

Integrative analysis of Illumina HumanMethylation450k data and exon-level RNAseq data using Epivizr. Regions of hypomethylation blocks obtained from TCGA data using the 450k array (bottom track) shown along with regions obtained from sequencing data (Hansen et al.) on independent samples. An MA plot (top) of exon-level RNA-seq data from the TCGA project over the same region (the MA transformation was obtained using the computed measurements tool in the Epiviz UI).