Browse > Article
http://dx.doi.org/10.3745/KIPSTD.2008.15-D.5.681

Discovery-Driven Exploration Method in Lung Cancer 2-DE Gel Images Using the Data Cube  

Shim, Jung-Eun (연세대학교 컴퓨터과학과)
Lee, Won-Suk (연세대학교 컴퓨터과학과)
Publication Information
The KIPS Transactions:PartD / v.15D, no.5, 2008 , pp. 681-690 More about this Journal
Abstract
In proteomics research, the identification of differentially expressed proteins observed under specific conditions is one of key issues. There are several ways to detect the change of a specific protein's expression level such as statistical analysis and graphical visualization. However, it is quiet difficult to handle the spot information of an individual protein manually by these methods, because there are a considerable number of proteins in a tissue sample. In this paper, using database and data mining techniques, the application plan of OLAP data cube and Discovery-driven exploration is proposed. By using data cubes, it is possible to analyze the relationship between proteins and relevant clinical information as well as analyzing the differentially expressed proteins by disease. We propose the measure and exception indicators which are suitable to analyzing protein expression level changes are proposed. In addition, we proposed the reducing method of calculating InExp in Discovery-driven exploration. We also evaluate the utility and effectiveness of the data cube and Discovery-driven exploration in the lung cancer 2-DE gel image.
Keywords
Proteome Informatics; Data Mining; On-Line Analytical Processing(OLAP); Two-Dimensional Electrophoresis;
Citations & Related Records
연도 인용수 순위
  • Reference
1 S. Y. Cho, K.-S. Park, J.E.Shim, M.-S.Kwon, K.H.Joo, W.S. Lee, J.Chang, H.Kim, H.C.Chung, H.O.Kim, Y.-K.Paik, An integrated proteome database for two-dimensional electrophoreses data analysis and laboratory information management system, Proteomics, 2, 1104-1113, 2002   DOI   ScienceOn
2 Gygi, SP, Rist, B., Gerber, SA, Turecek, F., Gelb, MH and Aebersold, R., Quantitative Analysis of Complex Protein Mixtures Using Isotope-Coded Affinity Tags, Nat.Biotech, Vol.17, No.10, pp.994-9, 1999   DOI   ScienceOn
3 Cagney, G. and Emili, A., De Novo Peptide Sequencing and Quantitative Profiling of Complex Protein Mixtures Using Mass-Coded Abundance Tagging, Nat Biotech., Vol.20, No. 2, 163-70, 2002   DOI   ScienceOn
4 S. O. Lim, S.-J. Park, W. Kim, S. G. Park, H.-J. Kim, Y. I. Kim, T.-S. Sohn, J.-H. Noh, G. Jung, Proteome Analysis of Hepatocellular Carcinoma, Biochemical and Biophysical Research Communications 291(4), 1031-1037, 2002   DOI   ScienceOn
5 Arnott D., O'Connell K.L., King K.L., Stults J.T., An Integrated Approach to Proteome Analysis: Identification of Protein Associated with Cardiac Hypertrophy, Analytical Biochemistry, 258, 1-18, 1998   DOI   ScienceOn
6 http://www.genebio.com/products/proteome_imaging.html
7 http://www.nonlinear.com/products/progenesis/samespots/overview.asp
8 Jane M.C.Oh, Brichory F., Puravs E., Kuick P., Wood C., Rouillard J.M., Tra J., Kandia S., Beer D., Hanash S., A database of protein expression in lung cancer, Proteomics, 1, 1303-1319, 2001   DOI
9 Rabilloud, T., Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains., Proteomics, 2, 3-10, 2002   DOI   ScienceOn
10 K..S..Park, Y..K..Jeon, S..Y..Cho, D. B..Kim, W..S..Lee, M.-S. Kwon, H. Kim, E. S. Yu, Gao V., Patterson D., B.-D. Han, Y.-K.Paik, Composite Analyses of Metabolic Profiles of Proteins That are Differentially Expressed in Hepatocellular Carcinoma, HUPO-The Second Congress of Human Proteome Organization, Montreal, Canada, 2003
11 Gray J., Chaudhuri S., Bosworth A., Layman A., Reichart D., Venkatrao M., Data Cube: A Relational Aggregation Operator Generalizing Group-By, Cross-Tab, and Sub-Totals, Data Mining and Knowledge Discovery, 1, 29-53, 1997   DOI
12 Agrawal R., Gupta A., Sarawagi S., Modeling multidimensional databases, Proc. of the 13th Int. Conference on Data Engineering, Birmingham, U.K., 1997   DOI
13 Sarawagi S., Agrawal R., Megiddo N., Discovery-driven Exploration of OLAP Data Cubes, Research Report RJ 10102(91918), IBM Almaden Research Center, January 1998
14 Jiawei Han and Micheline Kamber, DataMining: Concepts and Techniques, Morgan Kaufmann Publishers, 2000
15 Celis J. E., Rasmussen H. H., Gromov P., Olsen E., Madsen P., Leffers H., Honore B., Dejgaard K., Vorum H., Christensen D. B., $\{Phi}stergaard$ M., $\Hauns{varphi}$ A., Aagaard Jensen N., Celis A., Basse B., Lauridsen J. B., Ratz G. P., Andersen A. H., Walbum E., Kjaergaard I., Andersen I., Puype M., Van Damme J., Vandekerckhove J., The human keratinocyte two-dimensional protein database (update 1995): mapping components of signal transduction pathways, Electrophoresis, 16, 2177-2240, 1995   DOI   ScienceOn
16 Boer J.M., Huber W.K., Sultmann H., Wilmer F., von Heydebreck A., Haas S., Korn B., Gunawa B., Vente A., Fuzesi L., Vingron M., Poustka A., Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31, 500-element cDNA array, Genome Research, 11(11), 1161-1170, 2001