Microarray and gene-clustering analysis.

Tsung Hsien Tsai, Denise M. Milhorn, Shau Ku Huang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Human mast cells are capable of secreting a plethora of inflammatory mediators and cytokines that may play a pivotal role in innate immune and inflammatory responses. Activation of mast cells by antigen and immunoglobulin E (IgE) results in signaling, gene expression, and expression of inflammatory mediators. Although a variety of techniques have been used to evaluate mast cell biology, recent advances in molecular techniques have provided unprecedented tools to study these cells. The complimentary deoxyribonucleic acid (DNA) oligonucleotide microarray, or DNA-chip technology, allows simultaneous monitoring of gene expression, provides a format for identifying genes as well as changes in their activity on a whole genome scale, and potentially offers a global view of pathophysiologic changes. This chapter reviews the use of DNA-chip technology in studying the expression of genes (transcriptional profiling) in activated human mast cells obtained from cultured cord blood-derived mononuclear cells and comments on the use of bioinformatics on analysis of gene expression. The most powerful applications of transcriptional profiling involve identification of the common patterns of gene expression across many experiments using various gene-clustering analyses. Several techniques have been used for the analysis of gene-expression data including hierarchical clustering and self-organizing maps. In this chapter, a general laboratory protocol for array analysis currently being used in our laboratory and the use of bioinformatics is discussed. Although the focus is on Affymetrix oligonucleotide arrays, the techniques described are generally applicable to expression data generated using other array formats.

Original languageEnglish
Pages (from-to)165-174
Number of pages10
JournalMethods in molecular biology (Clifton, N.J.)
Volume315
Publication statusPublished - Feb 24 2006
Externally publishedYes

Fingerprint

Mast Cells
Cluster Analysis
Gene Expression
Gene Expression Profiling
Oligonucleotide Array Sequence Analysis
Computational Biology
Genes
DNA
Technology
Fetal Blood
Innate Immunity
Immunoglobulin E
Cell Biology
Genome
Cytokines
Antigens

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Microarray and gene-clustering analysis. / Tsai, Tsung Hsien; Milhorn, Denise M.; Huang, Shau Ku.

In: Methods in molecular biology (Clifton, N.J.), Vol. 315, 24.02.2006, p. 165-174.

Research output: Contribution to journalArticle

Tsai, Tsung Hsien ; Milhorn, Denise M. ; Huang, Shau Ku. / Microarray and gene-clustering analysis. In: Methods in molecular biology (Clifton, N.J.). 2006 ; Vol. 315. pp. 165-174.
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