1. Introduction to caIntegrator caBIG ® Molecular Analysis Tools Knowledge Center April 3, 2011

2. 2 (DW) (analysis) Motivation: Ad-hoc Linkages among caBIG ® Repositories

3. 3 (DW) (analysis) caIntegrator Brings Them Together

4. caIntegrator Overview 4 An data integration platform allows researchers to set up a custom, caBIG-compatible web portal to organize data into studies for analysis. Domains of data that are integrated Clinical data Genomic data (expression and copy number variation) Tumor imaging data in DICOM Cross-domain data query Data Visualization and Analysis

5. Why using caIntegrator? Target Users: Clinical/biomedical researchers performing translational research involving clinical, genomic, and imaging data Bioinformatics and clinical data management coordinators Multi-institutional data coordinating center informaticians Core Functions: Create and manage multiple studies Integrate clinical, genomic, and imaging data Perform cross-domain queries Perform sophisticated data analysis and visualization

6. Study Team Array Data Clinical Data Images Spread- sheet caIntegrator Study Team Image Annotations View Study Deploy Study Study Manager 2. Load data 3. Deploy study Public 1. Collect data 4. Query data 5. Analyze data How Does caIntegrator Work? Spread- sheet

7. 7 Web Interface: Study Summary

8. Study Data Management Clinical data Expression data Data from caArray Mapping data linking unique identifiers in clinical data and expression data Copy number data Data from caArray Mapping data linking unique identifiers in clinical data and copy number data Imaging data Data from NBIA (optional) Mapping data linking unique identifiers in clinical data and imaging data External link data 8

9. An Example: TCGA GBM Study 9

10. Create Study: Loading Clinical Data 10 Upload clinical data in csv format into caIntegrator Define data dictionary

11. Create Study: Loading Genomic Data 11

12. Create Study: Loading Imaging Data 12

13. Data Query and Analysis Query single or multiple data domains gender + gene list Save queries for future use Correlate clinical attributes with expression profiles Correlate clinical attributes or gene expression with survival Perform integrated genomic analysis using GenePattern modules Visualize data using the Integrated Genome Viewer (IGV) and NCI Heat Map Viewer 13

14. Query Clinical and Genomic Data 14

15. Kaplan-Meier Survival Analysis 15

16. Integrated Genomic Viewer: Global and Local View 16

17. 17 Public Data in caIntegrator Public Studies Released The Cancer Genome Atlas Glioblastoma Multiforme (TCGA GBM) study The Director’s Challenge Lung Study The REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) Therapeutically Applicable Research to Generate Effective Treatments (TARGET) Acute Lymphoblastic Leukemia (ALL) study TCGA Ovarian study

18. The Next Step: Accessing Online Resources for caIntegrator Molecular Analysis Tools Knowledge Center https://wiki.nci.nih.gov/x/R5GNAg caIntegrator User Forum https://cabig- kc.nci.nih.gov/Molecular/forums/viewforum.php?f=23 Tool Landing Pagehttps://cabig.nci.nih.gov/tools/caIntegrator Access to Demo caIntegrator Instance https://caintegrator2- train.nci.nih.gov/caintegrator2/workspace.action?https://caintegrator2- train.nci.nih.gov/caintegrator2/workspace.action?(Re gister from that site for a training account) Application SupportEmail: ncicb@pop.nci.nih.govncicb@pop.nci.nih.gov Phone: 301-451-4384 Toll-free: 888-478-4423 Web: http://ncicb.nci.nih.gov/NCICB/supporthttp://ncicb.nci.nih.gov/NCICB/support