The cBioPortal for Cancer Genomics was originally developed at Memorial Sloan Kettering Cancer Center (MSK). The public cBioPortal site is hosted by the Center for Molecular Oncology at MSK. The cBioPortal software is now available under an open source license through GitHub. The software is now developed and maintained by a multi-institutional team, consisting of MSK, the Dana Farber Cancer Institute, Princess Margaret Cancer Centre in Toronto, Children’s Hospital of Philadelphia, The Hyve in the Netherlands, and Bilkent University in Ankara, Turkey. cBioPortal consists of many components.
With the rapidly declining cost of next-generation sequencing, and major national and international efforts, including The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) (1), the field of cancer genomics continues to advance at an extraordinarily rapid pace. Data generated by these projects are, however, not easily or directly available to the cancer research community, hindering the translation of genomic data into new biologic insights, drugs, and clinical trials. The cBio Cancer Genomics Portal was specifically designed to address the unique data integration issues posed by large-scale cancer genomics projects and to make the raw data generated by large-scale cancer genomic projects more easily and directly available to the entire cancer research community.
A key feature of the cBio portal is its easy use. All features of the portal are therefore available through a streamlined 4-step web interface. Specifically, users are guided to select:
- a cancer study of interest,
- one or more genomic profiles, for example, mutations and copy number alterations
- a patient case set
- a gene set of interest: users can enter HUGO gene symbols, gene aliases, or Entrez Gene IDs and can enter arbitrary gene sets or pathways of interest
Users also have the option to automatically compute mutual exclusivity and co-occurrence between all pairs of genes. Finally, users have the option of performing cross-cancer queries, a simpler 2-step query, which requires only that users select “All Cancer Studies” and enter a gene set of interest.
- The increasingly useful and influential cBioPortal for Cancer Genomics provides a Web-based resource for Dana-Farber and other researchers to explore, visualize, analyze, and share multidimensional cancer genomics data sets from thousands of patients worldwide.
- The cBioPortal converts molecular profiling data from cancer tissues and cell lines into highly accessible genetic, epigenetic, gene expression, and proteomic events, for an unprecedented and ever growing level of interaction, collaboration, and data availability among investigators.
- The researchers across the globe can study and share trends in the mutations of various cancer types, with an eye toward new treatments and clinical trials. Originally designed as part of the National Cancer Institute’s Cancer Genome Atlas (TCGA), the cBioPortal is now used by tens of thousands of researchers.
- It helps the researchers to understand the molecular landscape of different cancer types.
cBioPortal provides “gene-based” visualizations and analyses, so that users can find mutated or altered genes and/or networks within a study of interest or across all studies. Starting a search is simple with the cBioPortal’s four-step “Query” web interface. Users select the desired:
- cancer study
- genomic profile(s), such as mutations and copy number alterations
- patient case set
- gene sets of interest
Gene sets can be entered manually or selected from pre-loaded cancer pathways derived from Pathway Commons