Genomic data analysis platform (geWorkbench)

Visit the geWorkbench section of the Molecular Analysis Tools Knowledge Center to submit questions, comments, feature requests, bug reports, and end-user requirements.

Visit the geWorkbench community Wiki for additional information and resources, view the use cases, and review the following geWorkbench training demos:

• Working with sets of data
• Gene expression profiling
• Hierarchical & SOM clustering

Genomic/clinical data on glioblastoma multiforme (GBM) and ovarian tumors
(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)

• Learn about the Cancer Gene Index
• Access the Cancer Gene Index data

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)

• Learn about VASARI
• Access VASARI data from the NCI-hosted instance of NBIA

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)

• Learn about REMBRANDT
• Access the REMBRANDT data

View other research data resources available through caBIG^®.

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).

• Learn more about this portal and the steps to conducting research
• Access NCI-hosted instance of REMBRANDT

• Harnessing the Power of Data-Sharing and Collaboration
• Frequently Asked Questions: geWorkbench
• Streamlining Genomics Research

geWorkbench is developed and maintained 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 geWorkbench and address any additional questions through the end user discussion forum.

geWorkbench 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 workflow tool (GenePattern): Analyze gene expression, proteomic, and SNP data; create multi-step analysis pipelines that enable in silico research.
• Genomic variation analyzer (caGWAS): Integrate, query, analyze, and report associations between genetic variations and disease, drug response, and other clinical outcomes.
• 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.