BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers.
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.
Jeong
Seul-Ki
SK
Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Sudaemoon-ku, Seoul 120-749, Korea.
Kwon
Min-Seok
MS
Lee
Eun-Young
EY
Lee
Hyoung-Joo
HJ
Cho
Sang Yun
SY
Kim
Hoguen
H
Yoo
Jong Shin
JS
Omenn
Gilbert S
GS
Aebersold
Ruedi
R
Hanash
Sam
S
Paik
Young-Ki
YK
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
D014408:Biomarkers, Tumor