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Open Access Highly Accessed Research article

Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

Yong Li1, Lili Liu1, Xi Bai1, Hua Cai1, Wei Ji1, Dianjing Guo2* and Yanming Zhu1*

Author Affiliations

1 Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin, China

2 State Key Lab of Agrobiotechnology and Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong

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BMC Bioinformatics 2010, 11:520  doi:10.1186/1471-2105-11-520

Published: 19 October 2010

Abstract

Background

Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data.

Results

In this study, we propose a new discretization method "bikmeans", and compare its performance with four other widely-used discretization methods using different datasets, modeling algorithms and number of intervals. Sensitivities, specificities and total accuracies were calculated and statistical analysis was carried out. Bikmeans method always gave high total accuracies.

Conclusions

Our results indicate that proper discretization methods can consistently improve gene regulatory network inference independent of network modeling algorithms and datasets. Our new method, bikmeans, resulted in significant better total accuracies than other methods.