A nonparametric likelihood ratio test to identify differentially expressed genes from microarray data.

Sankar Bokka, Sunil Mathur

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Microarray experiments contribute significantly to the progress in disease treatment by enabling a precise and early diagnosis. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The statistical methods currently used to analyse microarray data are inadequate, mainly due to the lack of understanding of the distribution of microarray data. We present a nonparametric likelihood ratio (NPLR) test to identify differentially expressed genes using microarray data. The NPLR test is highly robust against extreme values and does not assume the distribution of the parent population. Simulation studies show that the NPLR test is more powerful than some of the commonly used methods, such as the two-sample t-test, the Mann-Whitney U-test and significance analysis of microarrays (SAM). When applied to microarray data, we found that the NPLR test identifies more differentially expressed genes than its competitors. The asymptotic distribution of the NPLR test statistic and the p-value function is presented. The application of the NPLR method is shown, using both synthetic and real-life data. The biological significance of some of the genes detected only by the NPLR method is discussed.

Original languageEnglish (US)
Pages (from-to)267-276
Number of pages10
JournalApplied Bioinformatics
Volume5
Issue number4
DOIs
StatePublished - Jan 1 2006

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Microarrays
Genes
Microarray Analysis
genes
testing
Nonparametric Statistics
Early Diagnosis
early diagnosis
Demography
statistical analysis
statistics
methodology
Statistical methods
Experiments
Statistics
sampling

ASJC Scopus subject areas

  • Information Systems
  • Agricultural and Biological Sciences(all)
  • Computer Science Applications

Cite this

A nonparametric likelihood ratio test to identify differentially expressed genes from microarray data. / Bokka, Sankar; Mathur, Sunil.

In: Applied Bioinformatics, Vol. 5, No. 4, 01.01.2006, p. 267-276.

Research output: Contribution to journalArticle

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