BiomarkerDigger

A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers

Seul Ki Jeong, Min Seok Kwon, Eun Young Lee, Hyoung Joo Lee, Yun Cho Sang, Hoguen Kim, Shin Yoo Jong, Gilbert S. Omenn, Ruedi Aebersold, Sam Hanash, Young-Ki Paik

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

We have developed a proteome database (DB), BiomarkerDigger (http://biomarkerdigger.org) that automates data analysis, searching, and metadata-gathering function. The metadatagathering 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.

Original languageEnglish
Pages (from-to)3729-3740
Number of pages12
JournalProteomics
Volume9
Issue number14
DOIs
Publication statusPublished - 2009 Jul 1

Fingerprint

Proteome
Tumor Biomarkers
Databases
Plasmas
Biomarkers
Proteins
Proteomics
Tissue
Genetic Databases
Gene Ontology
Metadata
Ontology
Hepatocellular Carcinoma
Healthy Volunteers
Datasets
Neoplasms

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Jeong, Seul Ki ; Kwon, Min Seok ; Lee, Eun Young ; Lee, Hyoung Joo ; Sang, Yun Cho ; Kim, Hoguen ; Jong, Shin Yoo ; Omenn, Gilbert S. ; Aebersold, Ruedi ; Hanash, Sam ; Paik, Young-Ki. / BiomarkerDigger : A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. In: Proteomics. 2009 ; Vol. 9, No. 14. pp. 3729-3740.
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Jeong, SK, Kwon, MS, Lee, EY, Lee, HJ, Sang, YC, Kim, H, Jong, SY, Omenn, GS, Aebersold, R, Hanash, S & Paik, Y-K 2009, 'BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers', Proteomics, vol. 9, no. 14, pp. 3729-3740. https://doi.org/10.1002/pmic.200800593

BiomarkerDigger : A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. / Jeong, Seul Ki; Kwon, Min Seok; Lee, Eun Young; Lee, Hyoung Joo; Sang, Yun Cho; Kim, Hoguen; Jong, Shin Yoo; Omenn, Gilbert S.; Aebersold, Ruedi; Hanash, Sam; Paik, Young-Ki.

In: Proteomics, Vol. 9, No. 14, 01.07.2009, p. 3729-3740.

Research output: Contribution to journalArticle

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AU - Kim, Hoguen

AU - Jong, Shin Yoo

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AU - Hanash, Sam

AU - Paik, Young-Ki

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