Mariska Bierkens, Jochem Bijlard
tranSMART is an open source data warehouse and a web-based browsing application for translational research designed to integrate data from various domains (e.g. clinical and -omics data). Its focus is on data integration, exploration and visualization, and hypothesis generation. It includes utilities for creating quick data summaries, running advanced workflows and has a fully functional genome browser.
It is possible to select a specific subject cohort in tranSMART and export data for customised processing, data analysis and extensive querying, but tranSMART users may explore data at various levels without needing to become domain experts to interpret the data.
In this workshop Mariska Bierkens and Jochem Bijlard will help you reproduce results from an oncology paper published in Nature Communications¹ using the tranSMART data warehouse.
You will integrate basic clinical variables and large scale DNA copy number variation data measured with array CGH, and e.g. recreate survival curves and frequency plots presented in the paper.
Figure 1. TransMART user interface. Display of data in tree-overview, summary statistics, gridview and an advanced workflow analysis (aCGH survival).
¹ - Haan, JC et al (2014) Genomic landscape of metastatic colorectal cancer. Nature Communications. 5:5457 doi: http://dx.doi.org/10.1038/ncomms6457