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

Introduction to caIntegrator

caBIG® Molecular Analysis Tools

Knowledge Center

April 3, 2011

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(DW)

(DW)(DW)

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(analysis)

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Motivation: Ad-hoc Linkages among caBIG® Repositories

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(DW)

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(DW)

(analysis)

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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: ncicb@pop.nci.nih.gov

Phone: 301-451-4384

Toll-free: 888-478-4423

Web: http://ncicb.nci.nih.gov/NCICB/support