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Proteomics. 2009 Jul;9(14):3729-40. doi: 10.1002/pmic.200800593.

BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers.

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Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Sudaemoon-ku, Seoul 120-749, Korea.


We have developed a proteome database (DB), BiomarkerDigger ( 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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