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 language | English |
|---|---|
| Pages (from-to) | 3729-3740 |
| Number of pages | 12 |
| Journal | Proteomics |
| Volume | 9 |
| Issue number | 14 |
| DOIs | |
| Publication status | Published - 2009 Jul 1 |
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All Science Journal Classification (ASJC) codes
- Biochemistry
- Molecular Biology
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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 journal › Article
TY - JOUR
T1 - BiomarkerDigger
T2 - A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers
AU - Jeong, Seul Ki
AU - Kwon, Min Seok
AU - Lee, Eun Young
AU - Lee, Hyoung Joo
AU - Sang, Yun Cho
AU - Kim, Hoguen
AU - Jong, Shin Yoo
AU - Omenn, Gilbert S.
AU - Aebersold, Ruedi
AU - Hanash, Sam
AU - Paik, Young Ki
PY - 2009/7/1
Y1 - 2009/7/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=68049087901&partnerID=8YFLogxK
U2 - 10.1002/pmic.200800593
DO - 10.1002/pmic.200800593
M3 - Article
C2 - 19639590
AN - SCOPUS:68049087901
VL - 9
SP - 3729
EP - 3740
JO - Proteomics
JF - Proteomics
SN - 1615-9853
IS - 14
ER -