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CPTAC Proteomics Data on UCSC Genome Browser

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

CPTAC investigators have been working to extensively characterize the proteome content of breast, colorectal and ovarian cancer biospecimens that were initially sequenced by The Cancer Genome Atlas. Multi-dimensional 'omics data derived from these samples represent the largest collection of extensively characterized and integrated proteogenomic datasets to date. The ability to visualize and analyze CPTAC proteomics data in genomic context with other biomedical datasets will allow researchers lacking background in proteomics to interact with the data and develop novel hypotheses.

David Fenyo, Associate Professor at New York University Medical School comments, "By visualizing proteomics data in a genomic context we are not only making the data more available to the general scientific community, but are also allowing for the analysis of proteomics data alongside the wealth of genomics data to improve our understanding of cancer biology.”

The UCSC Genome Browser is an interactive web-based visualization with an associated database and tools that provide reference genome sequence and comprehensive annotation datasets for vertebrate and model organism genomes, with an emphasis on the human genome. The UCSC Genome Browser receives over a million hits a day from a wide range of biomedical researchers and students, from basic scientists to clinicians trying to understand the genetics of their patients. Genome Browser Director Jim Kent comments, "The Genome Browser integrates genomic data from a wide variety of sources; expanding to include proteomics data is enormously helpful."


To view an example browser session showing CPTAC data at PCNA, click here.

Additionally, where quantitative proteomics assays or antibodies are available, there are additional links from the CPTAC data to assist in the development of targeted experiments. Currently, all CPTAC data is made public prior to publication at the CPTAC Data Portal in both processed and unprocessed formats. The CPTAC data is presented in the browser as annotation tracks showing peptide identifications and quantification for each cancer. These data tracks are loaded dynamically in the Genome Browser from the CPTAC data hub at NCI when the user selects the hub from the Genome Browser public hub menu.

For more information regarding CPTAC, click here, and for additional information regarding UCSC Genome Browser, visit