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Related Experiment Video

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Murine Model of Allergen Induced Asthma
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A Gibbs sampling method to determine biomarkers for asthma.

Zhi-Jian Huang1, Qin-Hai Shen2, Yan-Sheng Wu3

  • 1Department of Emergency, Xiamen Hospital of Traditional Chinese Medicine, Xiamen 361009, Fujian, PR China.

Computational Biology and Chemistry
|February 15, 2017
PubMed
Summary

This study used Gibbs sampling to find new biomarkers for asthma, identifying key pathways like ubiquitin mediated proteolysis and cell cycle involved in the disease.

Keywords:
AsthmaGibbs samplingMarkov chainMolecular functionPathway enrichment analysis

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Area of Science:

  • Biochemistry and Bioinformatics
  • Genomics and Systems Biology

Background:

  • Asthma pathogenesis remains incompletely understood.
  • Identifying novel biomarkers and molecular mechanisms is crucial for effective diagnosis and treatment.

Purpose of the Study:

  • To identify potential biomarkers for asthma.
  • To elucidate the underlying molecular mechanisms of asthma using Gibbs sampling.

Main Methods:

  • Determined molecular functions (MFs) and transformed them into Markov chains (MCs).
  • Applied Gibbs sampling to obtain new MCs and computed average MF probabilities using Monte Carlo simulations.
  • Identified differentially expressed MFs and co-expressed genes, followed by pathway enrichment analysis.

Main Results:

  • Identified 5 differentially expressed MFs and 110 differentially expressed genes (DEGs).
  • Discovered 338 co-expressed genes significantly enriched in 6 pathways.
  • Ubiquitin mediated proteolysis and cell cycle pathways showed significant enrichment.

Conclusions:

  • Ubiquitin mediated proteolysis and cell cycle pathways are implicated in asthma development.
  • These pathways may offer potential targets for future asthma diagnostic and therapeutic strategies.