Ccle logo


Statistics

Cell Lines: 1457

Genes: 84,434

Unique Data Sets: 136,488

Mutation Entries: 1,159,663

Distribution Scores: 118,661,636

Methylation Scores: 411,948,577

Papers

Pharmacogenomic agreement between two cancer cell line data sets.

The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium
Nature doi:10.1038/nature15736   /  Nov 16, 2015

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Barretina Caponigro Stransky et al.
Nature doi:10.1038/nature11003   /  Mar 29, 2012

How To Use

Overview

Welcome!

The CCLE (Cancer Cell Line Encyclopedia) 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 over 1100 cell lines.

  • Gene expression data can be visualized as box plots or compared to other expression values in scatter plots. Each gene has multiple datasets and data identifiers. The five major dataset types are Copy Number, mRNA expression (Affy), RPPA, RRBS, and mRNA expression (RNAseq).
  • Gene Methylation can also be visualized through a bubble map.
  • Mutation data for individual cell lines is viewable and downloadable.

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.

Usage

Gene Visualization

Four different visualizations are available for genes: box plots, scatter plots, mutation data, and a bubble map. To view a gene's information, search for it from the front page. The search is auto completable. Below the box plot and scatter plot buttons to download axis specific data. The file will be tab delimited. To switch between visualizations, click the tab they are hosted in. The first tab is the box plot, the second tab is the scatter plot, the third tab is mutation data, and the fourth tab is methylation data.

Gene Info

The gene name, description and Entrez ID are listed at the top of the gene page. The Entrez ID links to the NCBI (National Center for Biotechnology Information) database for entry for the gene.

1

2

Box Plot

The first visualization displays the distribution of the genes expression data for a given dataset. The box plot is sorted and colored by average distribution of a gene's expression in a lineage. Lineages are composed of a number of cell lines from the same area or system of the body. The number next to the lineage name indicates how many cell lines are in the lineage. The highest average distribution is on the left and is colored red. The dashed line within a box is the mean.

23

3

The default dataset is mRNA expression(RNAseq). To change the displayed dataset, select a dataset from the drop down menu.

4

The graph is very interactive. You can zoom, pan, and deselect specific lineages. To zoom, click and drag over the area of the graph you want to zoom in on. To pan, select the pan tool from the the tool tip.

5

To save the graph as an image, select the 'download plot' icon from the tooltip.

The data for the plot can be viewed by selecting the 'save and edit in the cloud' button in the tooltip.

6

To hide certain lineages, click on their name in the legend. To show them again after hiding, click on them again.

Scatter Plot

The next visualization compares expression data for a gene against either a different dataset of itself or a dataset of another gene.

7

To different datasets of the same gene, select them from the two dropdown menus, and press 'Load Plot'. The first dropdown selects for the X Axis, while the second selects for the Y Axis.

8

To compare the gene's distribution against another gene, select the 'Different Gene' tab. To select the second gene, search for it using the search bar, and by clicking 'Search'. This search is also case insensitive, and autocomplete suggestions are also provided.

9

Pressing search will bring up another form for selecting different data sets. The X axis shows distributions of the original gene, while the Y axis shows distributions of the new selected gene.

10

The graph is very interactive. You can zoom, pan, and deselect specific lineages. To zoom,  click and drag over the area of the graph you want to zoom in on. To pan, select the pan tool from the the tool tip.

4

To save the graph as an image, select the 'download plot' icon from the tooltip.

The data for the plot can be viewed by selecting the 'save and edit in the cloud' button in the tooltip.

6

To hide certain lineages, click on their name in the legend. To show them again after hiding, click on them again.

At any point you switch between tabs or search for a different gene to compare to, and press the 'Load Plot' button to redisplay the wanted data.

Bubble Map

The third visualization displays methylation data for the gene. This visualization does not have a default option when the page loads.

11

To view methylation, select one, or multiple, lineages from the menu.

12

Multiple lineages can be selected.

13

The X axis displays the position of the Methylation data. The number before the colon is the chromosome, and the number after the colon is the position.

22

The Y Axis displays the Cell Line in which the Methylation was measured.

Bubble Size represents coverage, and bubble color represents methylation, with warmer colors being more methylated. Mousing over a specific bubble gives more specific information, such as coverage and methylation.

14

To scroll, use the arrow keys or the scroll bars.

Selecting a new lineage from the menu will replace the currently displayed bubble map.

Cell Line Info

The CCLE has over 1100 Cell Lines. To view a cell line's information, search for it from the front page. The search is auto completable.

15

Cell Line Info

The cell line name and lineage are listed at the top of the cell line page.

16

Mutation Data Table

The mutation data table displays a list of mutations specifics to the cell line or gene. To view this data, a user must be logged in, and have accepted the terms of access.

17

The table is fully sortable. To sort by a column, click on the arrow next to the column marker.

18

The table is also searchable. You can search for any data point, such as Hugo symbol, Gene, Cell Line, Chromosome, e.t.c, and the table will apply that filter.

19

Clicking on the Hugo Symbol or Entrez Gene ID of a mutation within a row will open up its corresponding database entry in the CCLE or the NCBI.

2

To export mutation data, click the 'Copy', 'CSV' or 'Excel' button to save. The 'Excel' button is not availible in Safari.

21

The data table scrolls horizontally, and can have multiple pages.

Terms of Access

Welcome to the Cancer Cell Line Encyclopedia. The information and materials ("Data") made available on this web site (www.broadinstitute.org/ccle), including the database of cancer cell lines genomic profiles and mutations (referred to collectively herein as the "Database") are made available to you (and your employing entity, where the download or use is within the scope of your employment by such entity- collectively "You") solely for internal research purposes. By accessing and viewing this Database, You agree to the following terms and conditions.

Use of Database:

You may download or use the Database only for internal research purposes. You may not download or use the Database, or any portion thereof, for any use not expressly authorized hereunder without prior written permission from Broad. You may not redistribute the Database or any portion thereof without prior written permission from Broad. You further agree that the Database shall not be used as the basis of a commercial product and that the Database shall not be rewritten or otherwise adapted to circumvent the need for obtaining permission for use of the Database other than as specified herein. No other rights to the Database, or to any computer software, database, copyright, trademark, patent, or other intellectual property rights owned by Broad or any contributor are conferred upon You by implication, estoppel, or otherwise, except as expressly granted herein. You acknowledge that ownership of the Database (including copyright where applicable) will remain with Broad and its contributors.

Confidentiality:

You agree to preserve, at all times, the confidentiality of Data pertaining to identifiable Data Subjects. In particular, You shall undertake not to use, or attempt to use the Data to deliberately compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. For purposes of this Agreement, Data Subject shall mean the person (irrespective of state of health) to whom Data refers and who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto.

Data Protection:

You agree that You shall not analyze or make any use of the Data in such a way that has the potential to: (i) lead to the identification of any Data Subject; or (ii) compromise the anonymity of any Data Subject in any way.

You agree to take all reasonable security precautions to keep the Data confidential, such precautions to be no less onerous than those applied in respect of your own confidential information.

Errors:

You agree to notify Broad of any errors detected in the Data.

Publications:

You agree to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the Data, and the role of the Broad in its distribution. You agree to use the acknowledgement wording provided for the relevant Data in its publication. You will also declare in any such work that those who carried out the original analysis and collection of the Data bear no responsibility for the further analysis or interpretation of it.

Termination of Agreement:

This Agreement will terminate immediately upon any breach by You. You accept that the changing ethical framework of human genetic research may lead to: (i) alteration of the provisions of this Agreement, in which case Broad shall notify You in writing via electronic mail of such alterations and You may choose to accept such alterations or to terminate this Agreement; or (ii) in extreme circumstances, the withdrawal of this Agreement.

Indemnification and Disclaimer of Warranties:

You are using this Database at Your own risk, and You hereby agree to hold Broad and its contributors and their trustees, directors, officers, employees, and affiliated investigators harmless for any third party claims which may arise from Your download or use of the Database or any portion thereof. The Database is a research database and is provided "as is". Broad does not represent that the Database is free of errors or bugs or suitable for any particular tasks.

ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS ARE DISCLAIMED. IN NO EVENT SHALL BROAD OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS DATABASE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Governing Law:

The terms and conditions herein shall be construed, governed, interpreted, and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the Database, You consent to the personal jurisdiction of, and venue in, the state and federal courts within Massachusetts with respect to Your download or use of the Database.

Bubble heatmap visualizer derived from the GTEx Portal

Original CCLE