title: A quantization method based on threshold optimization for microarray short time series.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Information Engineering Department, University of Padova, Padova, 35131, Italy. dicamill@dei.unipd.it
authors.forename: Barbara
authors.initials: B
authors.lastname: Di Camillo
authors.forename: Fatima
authors.initials: F
authors.lastname: Sanchez-Cabo
authors.forename: Gianna
authors.initials: G
authors.lastname: Toffolo
authors.forename: Sreekumaran K
authors.initials: SK
authors.lastname: Nair
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Trajanoski
authors.forename: Claudio
authors.initials: C
authors.lastname: Cobelli
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005188:False Negative Reactions; D005189:False Positive Reactions; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D016013:Likelihood Functions; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D011336:Probability; D012044:Regression Analysis; D049490:Systems Biology