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Introduction to caIntegrator
caBIG® Molecular Analysis Tools
Knowledge Center
April 3, 2011
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(DW)
(DW)(DW)
(DW)
(DW)
(analysis)
(analysis)
Motivation: Ad-hoc Linkages among caBIG® Repositories
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(DW)
(DW)
(DW)
(DW)
(analysis)
(analysis)
caIntegrator Brings Them Together
caIntegrator Overview
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• 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
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
Study Team
Array Data
Clinical Data
Images
Spread-sheet
caIntegrator
Study Team
Image AnnotationsView Study
Deploy Study
Study Manager
2. Load data2. Load data
3. Deploy study3. Deploy study
Public
1. Collect data1. Collect data
4. Query data4. Query data
5. Analyze data5. Analyze data
How Does caIntegrator Work?
Spread-sheet
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Web Interface: Study Summary
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
An Example: TCGA GBM Study
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Create Study: Loading Clinical Data
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• Upload clinical data in csv format into caIntegrator
• Define data dictionary
Create Study: Loading Genomic Data
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Create Study:Loading Imaging Data
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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
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Query Clinical and Genomic Data
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Kaplan-Meier Survival Analysis
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Integrated Genomic Viewer:Global and Local View
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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
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 Page https://cabig.nci.nih.gov/tools/caIntegrator
Access to Demo caIntegrator Instance
https://caintegrator2-train.nci.nih.gov/caintegrator2/workspace.action?(Register from that site for a training account)
Application Support Email: [email protected]
Phone: 301-451-4384
Toll-free: 888-478-4423
Web: http://ncicb.nci.nih.gov/NCICB/support