iGPSe: A Visual Analytic System for Integrative Genomic Based Cancer Patient Stratification

Hao Ding,Chao Wang,Kun Huang,Raghu Machiraju

Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied prognosis and response to treatment and likelihood for recurrence and metastasis. Recently, integrative genomics (or panomics) approaches are often adopted with the goal of combining multiple types of omics data to identify integrative biomarkers for stratification of patients into groups with different clinical outcomes.
Results: In this paper we present a visual analytic system called Interactive Genomics Patient Stratification explorer (iGPSe) which significantly
reduces the computing burden for biomedical researchers in the process of exploring complicated integrative genomics data. Our system integrates unsupervised clustering with graph and parallel sets visualization and allows direct comparison of clinical outcomes via survival analysis. Using a breast cancer dataset obtained from the The Cancer Genome Atlas (TCGA) project, we are able to quickly explore different combinations of gene expression (mRNA) and microRNA features and identify potential combined markers for survival
Conclusions: Visualization plays an important role in the process of stratifying given population patients. Visual tools allowed for the selection of possibly features across various datasets for the given patient population. We essentially made a case for visualization for a very important problem in translational informatics.

BioVis 2014 Information

Interactive Exploration of Spatial Distribution in Mass Spectrometry ImagingNeXO Web: An integrated ontology visualization application for modern web platformsTreemap Visualization of Personal Genomic ReportsHitWalker2: An interactive and queryable web-based framework for variant prioritization in precision medicineGWAS Viewer - a fast and interactive visualization for GWAS resultsConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug DiscoveryAn interactive visualisation tool for the hierarchical clustering of large data setsMCAweb: an interactive graphical tool for Multiresolution Correlation Analysis in single-cell dataGingr: Interactive visualization of large-scale phylogenies and multi-alignments.NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal ConnectivityLONGEVITY: A novel visualization platform for interpreting multidimensional gene expressionExploration of metagenome assemblies with an interactive visualization tool.