Oncotator is a web application for annotating human genomic point mutations and indels with data relevant to cancer researchers. Annotations are aggregated from the following resources:
- Gene, transcript, and functional consequence annotations using UCSC KnownGenes hg19 and mirBase reference sets.
- Common SNP annotations from dbSNP (includes data from 1000 Genomes project pilot 1, 2, and 3 studies).
- Site-specific protein annotations from UniProt.
- Druggable target data from DrugBank.
- Functional impact predictions from PolyPhen-2.
- Observed cancer mutation frequency annotations from COSMIC.
- Cancer gene and mutation annotations from the Cancer Gene Census.
- Significant amplification/deletion region annotations from Tumorscape and the TCGA Copy Number Portal.
- Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia.
- Significantly mutated gene annotations aggregated from published MutSig analyses.
- Cancer gene annotations from the Familial Cancer Database.
- Human DNA Repair Gene annotations from Wood et al.
Please see the help page for detailed information regarding all annotations.
Upload your input data below. Please note, only GRCh37/hg19 coordinates are supported and there is a maximum of 7500 alterations per input file. If you need additional help, please visit our help page or feel free to contact us directly.
Upload text file of mutations in Oncotator format.
Explore Oncotator's API format.
6 March 2015
We’re now published! Please see our Database-in-Brief article describing Oncotator, published in Human Mutation.
3 December 2014
Our new site is now in Beta... check it out here: http://www.broadinstitute.org/oncotator_beta, and give us feedback at email@example.com. If it appears down, please try back later.
3 November 2014
New website coming soon!
We've been hard at work updating the website and we hope to roll out a new version running Oncotator v1.3 under the hood soon. Users will be able to enjoy all the benefits of Oncotator v1.x without having to install the tool locally. In addition, we've re-written both the back and front-ends of the web application, which will allow the team to better maintain the site and add additional features. For a limited time after the rollout, users will be able the access the old site (using Oncotator v 0.4) with a different URL.
Stay tuned for more information.
27 June 2014
The public release of the standalone version is upon us!
The standalone version of Oncotator is free for non-profit use.
Oncotator Download and Install Instructions
4 January 2013 - Happy New Year
Happy New Year from the Oncotator Team!
Much is planned for Oncotator 2013, including:
- Standalone version of Oncotator -- Execute your own annotation runs from the command line
- Support for more file formats, both in and out
- Easy addition of annotation sources by users
15 October 2011 - Oncotator Resource Updates
The following resources have been updated:
- Oncotator v0.4.1.8