Data analysis (caIntegrator portal)
Access and conduct analyses on genomic and expression data from several large public datasets such as The Cancer Genome Atlas (TCGA), TARGET, REMBRANDT, the Director's Challenge Lung Cancer Study, and the CoCaNUT colon cancer study through the caIntegrator data analysis portal.
Currently available data
As of December 2010, the NCI-hosted instance of caIntegrator provided access to the following data:
- RNA expression data (CoCaNUT - Molecular Dissection of Colon Cancer)
- Gene expression for lung adenocarcinomas (Directorâ€™s Challenge Lung Study)
- Gene expression, copy number variation, and clinical outcomes (REMBRANDT)
- Gene expression and molecular data on pediatric patients with Acute Lymphoblastic Anemia (TARGET)
- Gene expression data and images from GBM patients with glioblastoma (The Cancer Genome Atlas - TCGA)
The caIntegrator application can be installed at your own organization for use with your own research data. To learn more, download, and install caIntegrator, please visit the caIntegrator application page.
Types of analysis
- Plot gene expression data
- Plot Kaplan-Meyer survival graphs, correlated with any available genomic information
- Visualize gene mutations (SNPs and copy number variations) in the gene or genome views
- View heatmaps showing gene expression and methylation data, somatic mutations, CNV
- Perform Principle Component Analysis (PCA) and use other tools from GenePattern to analyze gene expression and genomic data.
Use the caIntegrator portal
The best way to get started is to visit the NCI-hosted instance of caIntegrator and identify your areas of interest.
If additional help is required, please contact NCICB Application Support at firstname.lastname@example.org or review the following online resources: