Toward a comprehensive quantitative proteome database: Protein expression map of lymphoid neoplasms by 2-D DIGE and MS

Kazuyasu Fujii, Tadashi Kondo, Masayo Yamada, Keiji Iwatsuki, Setsuo Hirohashi

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Using 2-D DIGE, we constructed a quantitative 2-D database including 309 proteins corresponding to 389 protein spots across 42 lymphoid neoplasm cell lines. The proteins separated by 2-D PAGE were identified by MS and assigned to the expression data obtained by 2-D DIGE. The cell lines were categorized into four groups: those from Hodgkin's lymphoma (HL) (4 cell lines), B cell malignancies (19 cell lines), T cell malignancies (16 cell lines), and natural killer (NK) cell malignancies (3 cell lines). We characterized the proteins in the database by classifying them according to their expression level. We found 28 proteins with more than a 2-fold difference between the cell line groups. We also noted the proteins that allowed multidimensional separation to be achieved (1) between HL cells and other cells, (2) between the cells derived from B cells, T cells and NK cells, and (3) between HL cells and anaplastic large cell lymphoma cells. Decision tree classification identified five proteins that could be used to classify the 42 cell lines according to differentiation. These results suggest that the quantitative 2-D database using 2-D DIGE will be a useful resource for studying the mechanisms underlying the differentiation phenotypes of lymphoid neoplasms.

Original languageEnglish
Pages (from-to)4856-4876
Number of pages21
JournalProteomics
Volume6
Issue number17
DOIs
Publication statusPublished - Sep 2006

Fingerprint

Protein Databases
Proteome
Cells
Cell Line
Neoplasms
Proteins
Hodgkin Disease
Natural Killer Cells
T-cells
B-Lymphocytes
Databases
Anaplastic Large-Cell Lymphoma
T-Lymphocytes
Decision Trees
Decision trees
Lymphocytes
Phenotype

Keywords

  • 2-D DIGE
  • Classification
  • Database
  • Lymphoid neoplasm

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Toward a comprehensive quantitative proteome database : Protein expression map of lymphoid neoplasms by 2-D DIGE and MS. / Fujii, Kazuyasu; Kondo, Tadashi; Yamada, Masayo; Iwatsuki, Keiji; Hirohashi, Setsuo.

In: Proteomics, Vol. 6, No. 17, 09.2006, p. 4856-4876.

Research output: Contribution to journalArticle

Fujii, Kazuyasu ; Kondo, Tadashi ; Yamada, Masayo ; Iwatsuki, Keiji ; Hirohashi, Setsuo. / Toward a comprehensive quantitative proteome database : Protein expression map of lymphoid neoplasms by 2-D DIGE and MS. In: Proteomics. 2006 ; Vol. 6, No. 17. pp. 4856-4876.
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