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CCLE specifications


Unique identifier OMICS_03988
Alternative name Cancer Cell Line Encyclopedia
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.17
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Levi A. Garraway

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Publication for Cancer Cell Line Encyclopedia

CCLE citations


Multi omics profiling of younger Asian breast cancers reveals distinctive molecular signatures

Nat Commun
PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] RNA-Seq-derived gene expression data (TPM) from TCGA breast cancer, CCLE and GTEX normal breast samples were obtained from Omicsoft 2016 Q1 release, which consistently analyzed all datasets using the Omicsoft RSEM pipeline with the same library of gene models (Omicsof […]


Accurate identification of RNA editing sites from primitive sequence with deep neural networks

Sci Rep
PMCID: 5902551
PMID: 29662087
DOI: 10.1038/s41598-018-24298-y

[…] of the A-to-I ratio in 462 individuals, then compared the consistency of these methods. Furthermore, we performed the same comparison analysis on RNA-seq samples from ENCODE, Roadmap Epigenomics, and cancer cell line encyclopedia (CCLE) projects (Tables –).We down sampled the RNA-seq data of human brain reference data from the SEQC project to compare the overall runtime of DeepRed with the separat […]


A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

Cell Syst
PMCID: 5951639
PMID: 29655704
DOI: 10.1016/j.cels.2018.03.012

[…] e this application, we revisited data from a previously published chromatin profiling study that demonstrated how cancer-associated genetic alterations resulted in unique chromatin signatures (). The Cancer Cell Line Encyclopedia (CCLE) is a collection of more than 900 diverse cancer lines representing different tissues and sites of origin, and encompasses a wide variety of cancer driver mutations […]


Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment

Hum Genomics
PMCID: 5896091
PMID: 29642934
DOI: 10.1186/s40246-018-0150-x
call_split See protocol

[…] We downloaded unprocessed WES BAM files, which were available for 325 CCLE cell lines (Fig. ), from the CCLE project at the National Cancer Institute (NCI) Cancer Genomics Hub; these data are available at the NCI Genomic Data Commons (GDC) data portal []. All CCLE WES d […]


Investigation of model stacking for drug sensitivity prediction

BMC Bioinformatics
PMCID: 5872495
PMID: 29589559
DOI: 10.1186/s12859-018-2060-2

[…] In order to test our theory on real dataset, we obtain gene expression and normalized Area Under the Curve (AUC) values for the cell lines tested on the drug 17-AAG from the Cancer Cell Line Encyclopedia (CCLE) []. From the available 19,000 gene expressions we use RELIEFF [] to screen top 250 features. Similar to the synthetic case, we segregate 50 training samples into o […]


Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma

PLoS One
PMCID: 5771580
PMID: 29342193
DOI: 10.1371/journal.pone.0190664

[…] DNA Copy Number (41.6GB) Affy SNP data in the form of copy number by gene for 60 glioma cell lines was downloaded from the Cancer Cell Line Encyclopedia (CCLE) data portal at Copy Number Segment data from the Affymetrix SNP 6.0 platform for 526 GBM tumor and matched normal tissue samples was downloaded from The Canc […]


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CCLE institution(s)
The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Novartis Institutes for Biomedical Research, Cambridge, MA, USA; Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA; Novartis Institutes for Biomedical Research, Emeryville, CA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MA, USA; Sage Bionetworks, Seattle, WA, USA; Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
CCLE funding source(s)
The Cancer Cell Line Encyclopedia project was enabled by a grant from the Novartis Institutes for Biomedical Research. Additional funding support was provided by the National Cancer Institute, the Starr Cancer Consortium and the NIH Director’s New Innovator Award.

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