PMID- 16110157
OWN - NLM
STAT- MEDLINE
DCOM- 20051206
LR  - 20190902
IS  - 1064-3745 (Print)
IS  - 1064-3745 (Linking)
VI  - 315
DP  - 2006
TI  - Microarray and gene-clustering analysis.
PG  - 165-74
AB  - 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.
FAU - Tsai, Tsung-Hsien
AU  - Tsai TH
AD  - Division of Allergy and Clinical Immunology, Johns Hopkins University School of 
      Medicine, Baltimore, MD, USA.
FAU - Milhorn, Denise M
AU  - Milhorn DM
FAU - Huang, Shau-Ku
AU  - Huang SK
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
SB  - IM
MH  - Computational Biology
MH  - Fetal Blood/cytology
MH  - Gene Expression Profiling/*methods
MH  - Humans
MH  - Mast Cells/*physiology
MH  - *Multigene Family
MH  - Oligonucleotide Array Sequence Analysis/*methods
EDAT- 2005/08/20 09:00
MHDA- 2005/12/13 09:00
CRDT- 2005/08/20 09:00
PHST- 2005/08/20 09:00 [pubmed]
PHST- 2005/12/13 09:00 [medline]
PHST- 2005/08/20 09:00 [entrez]
AID - 1-59259-967-2:165 [pii]
AID - 10.1385/1-59259-967-2:165 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2006;315:165-74. doi: 10.1385/1-59259-967-2:165.