A landmark extraction method for protein 2DE gel images based on multi-dimensional clustering

Jung Eun Shim, Won Suk Lee

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Objective: Two-dimensional electrophoresis (2DE) is a separation technique that can identify target proteins existing in a tissue. Its result is represented by a gel image that displays an individual protein in a tissue as a spot. However, because the technique suffers from low reproducibility, a user should manually annotate landmark spots on each gel image to analyze the spots of different images together. This operation is an error-prone and tedious job. For this reason, this paper proposes a method of extracting landmark spots automatically by using a data mining technique. Method and material: A landmark profile which summarizes the characteristics of landmark spots in a set of training gel images of the same tissue is generated by extracting the common properties of the landmark spots. On the basis of the landmark profile, candidate landmark spots in a new gel image of the same tissue are identified, and final landmark spots are determined by the well-known A* search algorithm. Result and conclusions: The performance of the proposed method is analyzed through a series of experiments in order to identify its various characteristics.

Original languageEnglish
Pages (from-to)157-170
Number of pages14
JournalArtificial Intelligence in Medicine
Volume35
Issue number1-2
DOIs
Publication statusPublished - 2005 Sep 1

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Cluster Analysis
Gels
Tissue
Proteins
Data Mining
Electrophoresis
Data mining
Experiments

All Science Journal Classification (ASJC) codes

  • Medicine (miscellaneous)
  • Artificial Intelligence

Cite this

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A landmark extraction method for protein 2DE gel images based on multi-dimensional clustering. / Shim, Jung Eun; Lee, Won Suk.

In: Artificial Intelligence in Medicine, Vol. 35, No. 1-2, 01.09.2005, p. 157-170.

Research output: Contribution to journalArticle

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