Spherical self-organizing map as a helpful tool to identify category-specific cell surface markers

Tuoya, Yuh Sugii, Hitomi Satoh, Dongwei Yu, Yasaburo Matsuura, Heizo Tokutaka, Masaharu Seno

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

We analyzed gene expression profiles of five tumor cell lines (NB2a, NB41A3, C1300N18, BC3H1, and Neuro2a) derived from a category of nervous system using our originally developed cell surface marker DNA microarray in order to search for tumor-specific cell surface markers common to these cells. To visualize the expression patterns and to extract candidate genes of interest based on the expression profiles of several cell lines, we employed the clustering procedure of spherical self-organizing-map. As the result, three candidates of tumor-specific cell surface markers were picked up when the expression profiles were compared with that from normal brain tissue. RT-qPCR showed the expression of these genes was higher in tumor cells than in normal brain. Here we demonstrated the spherical self-organizing-map analysis should be useful to identify the candidates of cell surface markers common and specific to the group of cells or tissues of interest.

Original languageEnglish
Pages (from-to)414-418
Number of pages5
JournalBiochemical and Biophysical Research Communications
Volume376
Issue number2
DOIs
Publication statusPublished - Nov 14 2008

Fingerprint

Self organizing maps
Tumors
Cells
Brain
Genes
Tissue
Neurology
Microarrays
Gene expression
Neoplasms
Oligonucleotide Array Sequence Analysis
Tumor Cell Line
Transcriptome
DNA
Nervous System
Cluster Analysis
Gene Expression
Cell Line

Keywords

  • Cell surface marker
  • DNA microarray
  • Spherical self-organizing map
  • Tumor-specific

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology

Cite this

Spherical self-organizing map as a helpful tool to identify category-specific cell surface markers. / Tuoya; Sugii, Yuh; Satoh, Hitomi; Yu, Dongwei; Matsuura, Yasaburo; Tokutaka, Heizo; Seno, Masaharu.

In: Biochemical and Biophysical Research Communications, Vol. 376, No. 2, 14.11.2008, p. 414-418.

Research output: Contribution to journalArticle

Tuoya ; Sugii, Yuh ; Satoh, Hitomi ; Yu, Dongwei ; Matsuura, Yasaburo ; Tokutaka, Heizo ; Seno, Masaharu. / Spherical self-organizing map as a helpful tool to identify category-specific cell surface markers. In: Biochemical and Biophysical Research Communications. 2008 ; Vol. 376, No. 2. pp. 414-418.
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