A robust statistical method for detecting differentially expressed genes

Sunil Mathur

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

DNA microarray technology allows researchers to monitor the expressions of thousands of genes under different conditions, and to measure the levels of thousands of different DNA molecules at a given point in the life of an organism, tissue or cell. A wide variety of different diseases that are characterised by unregulated gene expression, DNA replication, cell division and cell death, can be detected early using microarrays. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The detection of differential gene expression under two different conditions is very important in biological studies, and allows us to identify experimental variables that affect different biological processes. Most of the tests available in the literature are based on the assumption of normal distribution. However, the assumption of normality may not be true in real-life data, particularly with respect to microarray data. A test is proposed for the identification of differentially expressed genes in replicated microarray experiments conducted under two different conditions. The proposed test does not assume the distribution of the parent population; thus, the proposed test is strictly nonparametric in nature. We calculate the p-value and the asymptotic power function of the proposed test statistic. The proposed test statistic is compared with some of its competitors under normal, gamma and exponential population setup using the Monte Carlo simulation technique. The application of the proposed test statistic is presented using microarray data. The proposed test is robust and highly efficient when populations are non-normal.

Original languageEnglish (US)
Pages (from-to)247-251
Number of pages5
JournalApplied Bioinformatics
Volume4
Issue number4
DOIs
StatePublished - Dec 12 2005

Fingerprint

Microarrays
Statistical methods
statistical analysis
Genes
Gene Expression
Biological Phenomena
DNA
genes
Normal Distribution
testing
Statistics
Oligonucleotide Array Sequence Analysis
DNA Replication
Gene expression
Cell Division
Population
statistics
Cell Death
Research Personnel
Demography

ASJC Scopus subject areas

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

Cite this

A robust statistical method for detecting differentially expressed genes. / Mathur, Sunil.

In: Applied Bioinformatics, Vol. 4, No. 4, 12.12.2005, p. 247-251.

Research output: Contribution to journalArticle

@article{5e7cdfc372394784a721757c837001f6,
title = "A robust statistical method for detecting differentially expressed genes",
abstract = "DNA microarray technology allows researchers to monitor the expressions of thousands of genes under different conditions, and to measure the levels of thousands of different DNA molecules at a given point in the life of an organism, tissue or cell. A wide variety of different diseases that are characterised by unregulated gene expression, DNA replication, cell division and cell death, can be detected early using microarrays. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The detection of differential gene expression under two different conditions is very important in biological studies, and allows us to identify experimental variables that affect different biological processes. Most of the tests available in the literature are based on the assumption of normal distribution. However, the assumption of normality may not be true in real-life data, particularly with respect to microarray data. A test is proposed for the identification of differentially expressed genes in replicated microarray experiments conducted under two different conditions. The proposed test does not assume the distribution of the parent population; thus, the proposed test is strictly nonparametric in nature. We calculate the p-value and the asymptotic power function of the proposed test statistic. The proposed test statistic is compared with some of its competitors under normal, gamma and exponential population setup using the Monte Carlo simulation technique. The application of the proposed test statistic is presented using microarray data. The proposed test is robust and highly efficient when populations are non-normal.",
author = "Sunil Mathur",
year = "2005",
month = "12",
day = "12",
doi = "10.2165/00822942-200504040-00004",
language = "English (US)",
volume = "4",
pages = "247--251",
journal = "Applied Bioinformatics",
issn = "1175-5636",
publisher = "Adis Press",
number = "4",

}

TY - JOUR

T1 - A robust statistical method for detecting differentially expressed genes

AU - Mathur, Sunil

PY - 2005/12/12

Y1 - 2005/12/12

N2 - DNA microarray technology allows researchers to monitor the expressions of thousands of genes under different conditions, and to measure the levels of thousands of different DNA molecules at a given point in the life of an organism, tissue or cell. A wide variety of different diseases that are characterised by unregulated gene expression, DNA replication, cell division and cell death, can be detected early using microarrays. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The detection of differential gene expression under two different conditions is very important in biological studies, and allows us to identify experimental variables that affect different biological processes. Most of the tests available in the literature are based on the assumption of normal distribution. However, the assumption of normality may not be true in real-life data, particularly with respect to microarray data. A test is proposed for the identification of differentially expressed genes in replicated microarray experiments conducted under two different conditions. The proposed test does not assume the distribution of the parent population; thus, the proposed test is strictly nonparametric in nature. We calculate the p-value and the asymptotic power function of the proposed test statistic. The proposed test statistic is compared with some of its competitors under normal, gamma and exponential population setup using the Monte Carlo simulation technique. The application of the proposed test statistic is presented using microarray data. The proposed test is robust and highly efficient when populations are non-normal.

AB - DNA microarray technology allows researchers to monitor the expressions of thousands of genes under different conditions, and to measure the levels of thousands of different DNA molecules at a given point in the life of an organism, tissue or cell. A wide variety of different diseases that are characterised by unregulated gene expression, DNA replication, cell division and cell death, can be detected early using microarrays. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The detection of differential gene expression under two different conditions is very important in biological studies, and allows us to identify experimental variables that affect different biological processes. Most of the tests available in the literature are based on the assumption of normal distribution. However, the assumption of normality may not be true in real-life data, particularly with respect to microarray data. A test is proposed for the identification of differentially expressed genes in replicated microarray experiments conducted under two different conditions. The proposed test does not assume the distribution of the parent population; thus, the proposed test is strictly nonparametric in nature. We calculate the p-value and the asymptotic power function of the proposed test statistic. The proposed test statistic is compared with some of its competitors under normal, gamma and exponential population setup using the Monte Carlo simulation technique. The application of the proposed test statistic is presented using microarray data. The proposed test is robust and highly efficient when populations are non-normal.

UR - http://www.scopus.com/inward/record.url?scp=28444455946&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=28444455946&partnerID=8YFLogxK

U2 - 10.2165/00822942-200504040-00004

DO - 10.2165/00822942-200504040-00004

M3 - Article

VL - 4

SP - 247

EP - 251

JO - Applied Bioinformatics

JF - Applied Bioinformatics

SN - 1175-5636

IS - 4

ER -