Broad-Novartis 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 CCLE is an ongoing project and some data are not complete yet. The CCLE website is subject to periodic changes and improvements. Please visit regularly!


This project is funded by Novartis.


News / Events

Nov 12, 2013: The Gene Set Enrichment Analysis (GSEA) is not currently able to run due to server issues. Engineers are working on the problem. 

Sep 30, 2013: The CCLE can now upload data directly to GenomeSpace. To learn more, see the GenomeSpace blog  more...

Sep 18, 2013: The portal will be unavailable from Thursday October 17 through Sunday October 20th for server maintenance. 

Aug 6, 2013: The problems with the GeneNeighbors and Differential Expression (CMS) analyses have been corrected. All systems are functioning normally once again. 

Aug 5, 2013: Due to a database issue, the GeneNeighbors and Differential Expression (CMS) analyses are not currently working. We have engineers trying to resolve the problem and hope to have this fixed shortly. 

May 20, 2013: The server problem has been resolved. Differential Expression, Gene Set Enrichment Analysis (GSEA) and sample browsing are working once again. 

May 17, 2013: There is currently a problem with accessing cell line annotations from the CCLE database. As a result browsing cell line annotations, GSEA and differential expression analysis are not currently working. We are working to resolve the problem as quickly as possible. 

New User?

Please register for full access to the data and analyses tools CCLE provides.


Terms of Access   Register

Tutorials / Manuals

Tutorials, analysis descriptions and other documentation is available at:
HELP > DOCUMENTS

Frequently Altered Genes

Tag clouds summarizing genes frequently altered in the datasets of this portal are available in the
Mutation tag cloud

Publications

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity,  Barretina Caponigro Stransky et al., Nature 483, 603-307, 2012

All Publications

Complementary Resources

Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines.

The Cancer Therapeutic Response Portal provides profiles of the impact of a small-molecule collection of 185 compounds on a panel of 242 cancer cell lines

The Genotype-Tissue Expression project (GTEx) aims to create a comprehensive public atlas of gene expression and regulation across multiple human tissues

What you can do on this portal

Search for information

Enter a keyword to search for genes, news items and publications. Search results for a gene include links to annotations and analyses.

Data Sets

Browse, analyze and download studies and data sets.

BROWSE   > DATA

Analysis Tools

The portal provides the following analysis tools:

Integrative Genomics Viewer (IGV)
Visualize a data set in the Integrative Genomics Viewer (IGV), a high-performance visualization tool for interactive exploration of large integrated data sets.

Differential Expression Analysis
Find genes that are significantly differentially expressed between two user-defined classes of samples from an expression data set available on this portal.

Gene co-expression
View the top 20 genes in a data set that are co-expressed with a gene of interest.

Gene Set Enrichment Analysis (GSEA)
Find pathway gene sets correlated with a gene of interest. Domain experts curate the pathway gene sets based on data from several online pathway databases.

ANALYSIS TOOLS

Sample Sets

Create your own sample sets based on a large number of available criteria and use them in differential expression analysis.
CREATE SAMPLE SETS