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

TitleBiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers
Publication TypeJournal Article
Year of Publication2009
AuthorsJeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S, Paik YK
JournalProteomics
Volume9
Pagination3729-40
Date PublishedJul
PMID19639590
Keywords*Databases, Protein, *Software, Computational Biology/methods, Humans, Models, Theoretical, Neoplasms, Plasma Cell/*metabolism, Proteomics/*methods, Tumor Markers, Biological/*analysis, User-Computer Interface
AbstractWe 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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