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An integrated proteome database for two‐dimensional electrophoresis data analysis and laboratory information management system
Author(s) -
Cho Sang Yun,
Park KangSik,
Shim Jung Eun,
Kwon MinSeok,
Joo Kil Hong,
Lee Won Suk,
Chang Joon,
Kim Hoguen,
Chung Hyun Cheol,
Kim Hyun Ok,
Paik YoungKi
Publication year - 2002
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/1615-9861(200209)2:9<1104::aid-prot1104>3.0.co;2-q
Subject(s) - proteome , computer science , protein data bank (rcsb pdb) , database , information retrieval , interface (matter) , data mining , bioinformatics , biology , biochemistry , bubble , maximum bubble pressure method , parallel computing
We describe an integrated proteome database, termed Yonsei Proteome Research Center Proteome Database (YPRC-PDB) which can store, retrieve and analyze various information including two-dimensional electrophoresis (2-DE) images and associated spot information that were obtained during studies of hepatocellular carcinoma (HCC). YPRC-PDB is also designed to perform as a laboratory information management system that manages sample information, clinical background, conditions of both sample preparation and 2-DE, and entire sets of experimental results. It also features query system and data-mining applications, which are amenable to automatically analyze expression level changes of a specific protein and directly link to clinical information. The user interface is web-based, so that the results from other laboratories can be shared effectively. In particular, the master gel image query is equipped with a graphic tool that can easily identify the relationship between the specific pathological stage of HCC and expression levels of a potential marker protein on the master gel image. Thus, YPRC-PDB is a versatile integrated database suitable for subsequent analyses. The information in YPRC-PDB is updated easily and it is available to authorized users on the World Wide Web (http://yprcpdb.proteomix.org/ approximately damduck/).