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SIEGE: Smoking Induced Epithelial Gene Expression Database.

Vishal Shah1, Sriram Sridhar, Jennifer Beane

  • 1Bioinformatics Program, College of Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA. vshah@bu.edu

Nucleic Acids Research
|December 21, 2004
PubMed
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The Smoking Induced Epithelial Gene Expression (SIEGE) database compiles gene expression data from airway cells of smokers and non-smokers. This resource aids research into how cigarette smoke impacts gene expression in the human airway.

Area of Science:

  • Pulmonary Medicine
  • Genomics
  • Bioinformatics

Background:

  • Cigarette smoking significantly impacts respiratory health.
  • Understanding molecular changes in airway epithelium is crucial for translational research.
  • Gene expression profiling provides insights into cellular responses to environmental exposures.

Purpose of the Study:

  • To establish the Smoking Induced Epithelial Gene Expression (SIEGE) database.
  • To support research on gene expression alterations in the airway epithelium due to cigarette smoke.
  • To provide a centralized resource for analyzing gene expression data from diverse smoking groups.

Main Methods:

  • RNA isolation from human intra-thoracic airway epithelium of current-, former-, and never-smokers.
  • Gene expression profiling using Affymetrix HG-U133A Genechips.

Related Experiment Videos

  • Data management and analysis utilizing a web-based database (SIEGE), PERL scripts, and the R statistical package.

    • Main Results:

    • The SIEGE database successfully integrates microarray data with patient information.
    • Quality control, data processing, and filtering are performed using integrated PERL scripts.
    • Statistical analyses including t-tests, correlation coefficients, and hierarchical clustering are executable via the database interface.

    Conclusions:

    • The SIEGE database serves as a valuable clinical and research resource.
    • It facilitates the analysis of gene expression changes induced by cigarette smoke.
    • The database links to external gene resources, enhancing its utility for researchers.