What is the use of OncoKB database
This article mainly introduces the use of the OncoKB database, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.
OncoKB collects genomic variation information of clinical significance related to tumorigenesis and development, and provides detailed information about its corresponding biological effects, drug interactions, prognosis and therapeutic significance for each variation.
The web address of the database is as follows
Http://oncokb.org/
The database focuses on genes and provides information about the variation of each gene, related tumor types, experimental evidence, and so on, as shown below.
According to the source and credibility of the experimental evidence, it is divided into different levels shown in the following figure.
Among them, level1 and level 2A are genomic variants of clinical significance. Through the Actionable Genes menu, we can query the interaction information between genomic variation and drugs, as shown below.
Click on each gene ID to view all the genomic variations on that gene, which can be divided into two categories
Clinically Relevant Alterations
All Annotated Alterations
Take ABL1 as an example, as shown below
Through the Cacner Genes menu, you can query the list of proto-oncogenes and tumor suppressor genes, as shown below
In addition to the query function, the database also provides a command-line tool for annotating its own genomic variation information and supporting annotations of SNV, CNV, fusion genes and other information. the tool is called oncokb-annotator and can be found at the following website
Https://github.com/oncokb/oncokb-annotator
The information in this database has been integrated into cBioPortal, which can help scientists to better carry out cancer research.
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