Census of Somatic Mutations in Cancer (COSMIC)
"COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer."
International Cancer Genome Consortium (ICGC)
"The ICGC goal is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe."
Oncomine
The Cancer Genome Atlas Project (TCGA)
- TCGA HomepageStarting point for information on The Cancer Genome Atlas (TCGA) Project, including up-to-date information, news/announcements and links to project data
- Genomic Data Commons (GDC)GDC is TCGA data portal, as well as housing other human genomic datasets.
- cBioPortalcBioPortal provides a simple interface for analysis of TCGA and other cancer genomic datasets.
- MorpheusMorpheus provides tools for analysis of TCGA samples without needing to download/upload TCGA datasets.
- Broad FirehoseThe Broad Firehose provides analyses of interpreted and summarized data.
Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
TARGET: Therapeutically Applicable Research To Generate Effective Treatments
TARGET applies a comprehensive genomic approach to determine molecular changes that drive childhood cancers. Investigators form a collaborative network to facilitate discovery of molecular targets and translate those findings into the clinic. TARGET is managed by NCI’s Office of Cancer Genomics and Cancer Therapy Evaluation Program.
Cancer at the Systems Level Workshop
These are materials to be used during the Bioinformatics Basics workshop.
Cancer Cell Line Encyclopedia (CCLE)
"The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines."
The Connectivity Map (CMap)
"The Connectivity Map (also known as cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes. You can learn more about cmap from [the cmap team's] papers in Science and Nature Reviews Cancer.
This web interface provides access to the current version (build 02) of Connectivity Map which contains more than 7,000 expression profiles representing 1,309 compounds. It is designed to allow biologists, pharmacologists, chemists and clinical scientists to use cmap without the need for any specialist ability in the analysis of gene-expression data."
Tutorials, credits/attributions and more can be found on the Broad Institute's website:
Cancer at the Systems Level Literature
The Cancer Genome Atlas Publications and Collections: