Oncotator

 What is Oncotator?

Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.

How does Oncotator work?

Annotations are aggregated from the following resources:

Genomic Annotations

• 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).

Protein Annotations

• Site-specific protein annotations from UniProt.
• Druggable target data from DrugBank.
• Coming soon:  Functional impact predictions from PolyPhen-2.

Cancer Annotations

• 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.

How do I use Oncotator?

A standalone version of Oncotator is being developed.  Check back here for updates.

In the meantime, a web-based version of Oncotator is available at http://www.broadinstitute.org/oncotator