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
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.
Dec 7, 2012: CCLE Downtime: The CCLE may be unavailable all day (EST) on December 15th due to electrical work at the Broad Institute.
Nov 9, 2012: CCLE Downtime. The CCLE will be unavailable on November 13th from 11am to 3pm EST for system maintenance at the Broad Institute
Nov 7, 2012: New feature: deep links to gene pages. You can now link directly to gene pages from other applications and portals using urls that include the gene symbol like this http://www.broadinstitute.org/ccle/gene/FGFR3
Oct 19, 2012: Gene expression analyses for the updated datasets are now functioning properly and the expression and copy number plots on the gene pages have been updated.
Oct 18, 2012: As part of the process for uploading the new datasets, analyses on the CCLE Gene Expression datasets are not functioning at the moment (Differential Expression, GSEA and GeneNeighbors). We expect to correct this problem shortly.
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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 |
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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
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