title: BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers.
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.
authors.affiliation: Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Sudaemoon-ku, Seoul 120-749, Korea.
authors.forename: Seul-Ki
authors.initials: SK
authors.lastname: Jeong
authors.forename: Min-Seok
authors.initials: MS
authors.lastname: Kwon
authors.forename: Eun-Young
authors.initials: EY
authors.lastname: Lee
authors.forename: Hyoung-Joo
authors.initials: HJ
authors.lastname: Lee
authors.forename: Sang Yun
authors.initials: SY
authors.lastname: Cho
authors.forename: Hoguen
authors.initials: H
authors.lastname: Kim
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Sam
authors.initials: S
authors.lastname: Hanash
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis*; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008962:Models, Theoretical; D054219:Neoplasms, Plasma Cell / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D014408:Biomarkers, Tumor