BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers |
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| Authors: | Seul‐Ki Jeong Min‐Seok Kwon Eun‐Young Lee Hyoung‐Joo Lee Sang Yun Cho Hoguen Kim Jong Shin Yoo Gilbert S. Omenn Ruedi Aebersold Sam Hanash Young‐Ki Paik |
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| Affiliation: | 1. Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Sudaemoon‐ku, Seoul, Korea;2. Department of Pathology, Yonsei University College of Medicine, Yonsei University, Sudaemoon‐ku, Seoul, Korea;3. Korea Basic Science Institute, Daejeon, Korea;4. Departments of Internal Medicine and Human Genetics and Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, USA;5. Institute for Systems Biology, Seattle, WA, USA;6. Institute of Molecular Systems Biology, ETH Zurich;7. and Faculty of Sciences, University of Zurich, Switzerland;8. Fred Hutchinson Cancer Research Center, Seattle, WA, USA |
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| Abstract: | We have developed a proteome database (DB), BiomarkerDigger ( http://biomarkerdigger.org ) that automates data analysis, searching, and metadata‐gathering function. The metadata‐gathering function searches proteome DBs for protein–protein interaction, Gene Ontology, protein domain, Online Mendelian Inheritance in Man, and tissue expression profile information and integrates it into protein data sets that are accessed through a search function in BiomarkerDigger. This DB also facilitates cross‐proteome comparisons by classifying proteins based on their annotation. BiomarkerDigger highlights relationships between a given protein in a proteomic data set and any known biomarkers or biomarker candidates. The newly developed BiomarkerDigger system is useful for multi‐level synthesis, comparison, and analyses of data sets obtained from currently available web sources. We demonstrate the application of this resource to the identification of a serological biomarker for hepatocellular carcinoma by comparison of plasma and tissue proteomic data sets from healthy volunteers and cancer patients. |
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| Keywords: | BiomarkerDigger Database HUPO Plasma proteome |
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