A quantization method based on threshold optimization for microarray short time series.
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.
Di Camillo
Barbara
B
Information Engineering Department, University of Padova, Padova, 35131, Italy. dicamill@dei.unipd.it
Sanchez-Cabo
Fatima
F
Toffolo
Gianna
G
Nair
Sreekumaran K
SK
Trajanoski
Zlatko
Z
Cobelli
Claudio
C
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