Genomic data analysis tool (GenePattern)
Perform sophisticated analysis on gene expression, proteomics, and SNP data using GenePattern. The web-based interface makes it simple for researchers to create multi-step analysis pipelines that enable in silico research.
- Watch the introductory presentation for a full capabilities overview
What would you like to do?
Learn more about this application
Visit the GenePattern section of the Molecular Analysis Tools Knowledge Center to submit questions, comments, feature requests, bug reports, and end-user requirements. You will also find the following resources:
- View the video on getting started with GenePattern
- Visit the GenePattern community wiki for more information and additional resources
- Explore the GenePattern FAQ to answer questions on topics ranging from instillation through integration
Access gene expression and other research data
Clinical and genomic data from translational research studies
(Available through TCGA)
- Learn about The Cancer Genome Atlas (TCGA) project
- Visit the TCGA Data Portal website
- Access the TCGA data
Gene expression/genomic characterizations and gene sequencing data for acute lymphoblastic and myeloid leukemias (ALL and AML), neuroblastoma, osteosarcoma, and high-risk Wilms tumor in children
(Available through TARGET)
- Learn about the TARGET project
- Visit the TARGET website
- Visit the TARGET Data Portal
- Browse the open-access TARGET data
- Apply for authorized access to the controlled-access TARGET data
- Access the TARGET data through the Authorized Access system
Human genes that have associations with cancer
(Available through the Cancer Gene Index)
Microarray gene expression data across a variety of cancers
(Available through NCI-hosted instance of caArray)
- Learn more about caArray
- Review a complete list of all available microarray datasets
- Register for free access to download and analyze this data
- Sample Data: GlaxoSmithKline has generated and donated SNP and expression data for over 300 cancer cell lines and made this information available through caArray.
Pre-surgical brain tumor MRI images matched to gene expression data
(Available through VASARI)
Prostate and breast cancer SNPs
(Available through the CGEMS)
- Learn about the Cancer Genetic Markers of Susceptibility (CGEMS) project
- Visit the CGEMS Data Portal website
- Apply for authorized access to CGEMS data
- Access the CGEMS data through the Authorized Access system
Primary brain tumor data matched to molecular and clinical data
(Available through REMBRANDT)
View other research data resources available through caBIG®.
Conduct research that correlates genomic and expression data with outcomes
Examine gene and chromosomal information, analyze expression data, and correlate this information with clinical outcomes data from the TCGA, REMBRANDT, and TARGET programs using the caBIG® Molecular Analysis Portal (CMA).
- Learn more about this portal and the steps to getting access and conducting research
- Access the CMA Portal
Correlate genomic and expression data with outcomes using analytical tools from the NCI-hosted instance of caIntegrator and data from TCGA, TARGET, REMBRANDT, the Director's Challenge Lung Cancer Study, and the CoCaNUT colon cancer study.
- Learn more about this portal and the steps to conducting research
- Access the NCI-hosted instance of caIntegrator
Examine gene expression, gene copy number data, and clinical outcomes from glioma patients using the REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT).
Read more about this application
- GenePattern: Integrated Genomics
- GenePattern case studies (Harvard-Partners Center for Genetics and Genomics and MIT)
- Bio-IT World: GenePattern Platform Integrates Genomics Analysis
- Case Study: GenePattern at Harvard-Partners Center for Genetics and Genomics
- Case Study: GenePattern Used to Teach Atomistic Modeling at MIT
- MIT News: Think Small! Think Quickly! Atomistic Model Helps Students Visualize Nanoscale Problems
- Nucleic Acids Research: Implementation of GenePattern within the Stanford Microarray Database
Review advanced resources and support options
GenePattern is supported by the Integrative Cancer Research (ICR) Workspace, which works to produce interoperable tools and resources to assist researchers in the analysis of molecular and genomic data.
caBIG® offers a number of support options for those learning about and deploying caBIG® tools and resources.
- Get additional help from Support Service Providers.
- Learn from others using GenePattern and address any additional questions through the end user discussion forum.
GenePattern is part of a collection of life science software tools designed to facilitate the discovery of the next generation of cancer diagnostics and therapeutics. Other applications and infrastructure of interest include:
- Genomic data analysis platform (geWorkbench): Analyze genomic data using desktop tools for the management, analysis, visualization, and annotation of microarray-based gene expression and sequence data.
- Genomic variation analyzer (caGWAS): Integrate, query, analyze, and report associations between genetic variations and disease, drug response, and other clinical outcomes.
- Nanoparticle annotation portal (caNanoLab): Support annotation of nanoparticles and share nanotechnology material characterizations and association protocols.
- Microarray data management system (caArray): Support annotation and exchange of array data; integrate array data with clinical, imaging, tissue, and other functional genomics data.
- Data analysis portal (caIntegrator): Access and analyze clinical and experimental data across multiple clinical trials and studies.
- Molecular analysis portal (CMA): Find novel correlations between data and observations using analytical tools that help to visualize and integrate genomic data with corresponding clinical information.
