A quantization method based on threshold optimization for microarray short time series

Barbara Di Camillo, Fatima Sanchez-Cabo, Gianna Toffolo, Sreekumaran K. Nair, Zlatko Trajanoski, Claudio Cobelli

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

Background: Reconstructing regulatory networks from gene expression profiles is a challenging problem of functional genomics. In microarray studies the number of samples is often very limited compared to the number of genes, thus the use of discrete data may help reducing the probability of finding random associations between genes. Results: A quantization method, based on a model of the experimental error and on a significance level able to compromise between false positive and false negative classifications, is presented, which can be used as a preliminary step in discrete reverse engineering methods. The method is tested on continuous synthetic data with two discrete reverse engineering methods: Reveal and Dynamic Bayesian Networks. Conclusion: The quantization method, evaluated in comparison with two standard methods, 5% threshold based on experimental error and rank sorting, improves the ability of Reveal and Dynamic Bayesian Networks to identify relations among genes.

Original languageEnglish (US)
Article numberS11
JournalBMC bioinformatics
Volume6
Issue numberSUPPL.4
DOIs
StatePublished - Dec 1 2005

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Fingerprint Dive into the research topics of 'A quantization method based on threshold optimization for microarray short time series'. Together they form a unique fingerprint.

  • Cite this

    Di Camillo, B., Sanchez-Cabo, F., Toffolo, G., Nair, S. K., Trajanoski, Z., & Cobelli, C. (2005). A quantization method based on threshold optimization for microarray short time series. BMC bioinformatics, 6(SUPPL.4), [S11]. https://doi.org/10.1186/1471-2105-6-S4-S11