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

Publication Type:

Journal Article

Source:

Proteomics, Volume 9, Issue 14, p.3729-40 (2009)

Keywords:

2009, Center-Authored Paper, Computational Biology, Databases, Protein, Humans, Models, Theoretical, Neoplasms, Plasma Cell, PROTEOMICS, Public Health Sciences Division, Software, Tumor Markers, Biological, User-Computer Interface

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.