Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs

Erin M. Conlon, Patrick Eichenberger, Jun S. Liu

Research output: Contribution to journal › Article

Abstract

We present a hierarchical Bayes model for determining genes in the sporulation pathway of Bacillus subtilis (B. subtilis) using two complementary replicated cDNA microarray experimental designs. The first design involves the mutation of a transcription factor, Sigma factor E (σE), and the second is an overexpression of this factor. We first normalize the microarray data using a rank invariant method. Genes found to be overexpressed in both experimental designs are further examined experimentally to determine their role in the sporulation pathway. Through statistical and experimental methods we found 181 genes that had not been previously described as controlled by σE. We identify the chromosome locations of clusters of σE-controlled genes using a nearest neighbor scan-statistic, and determine B. subtilis functional categories that are over-represented in subsets of expressed genes.

Original languageEnglish (US)
Pages (from-to)1-18
Number of pages18
JournalJournal of Multivariate Analysis
Volume90
Issue number1 SPEC. ISS.
DOIs
StatePublished - Jul 2004

Fingerprint

CDNA Microarray
Microarrays
Genes
Gene
Experiment
Bacilli
Experimental design
Experiments
Design of experiments
Pathway
Hierarchical Bayes
Scan Statistic
Normalize
Transcription factors
Chromosomes
Transcription Factor
Microarray Data
Chromosome
Nearest Neighbor
Mutation

Keywords

  • Bayesian models
  • CDNA microarrays
  • Functional category
  • Gene location cluster
  • MCMC
  • Scan statistics

ASJC Scopus subject areas

  • Statistics, Probability and Uncertainty
  • Numerical Analysis
  • Statistics and Probability

Cite this

Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. / Conlon, Erin M.; Eichenberger, Patrick; Liu, Jun S.

In: Journal of Multivariate Analysis, Vol. 90, No. 1 SPEC. ISS., 07.2004, p. 1-18.

Research output: Contribution to journal › Article

Conlon, EM, Eichenberger, P & Liu, JS 2004, 'Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs', Journal of Multivariate Analysis, vol. 90, no. 1 SPEC. ISS., pp. 1-18. https://doi.org/10.1016/j.jmva.2004.02.007
Conlon EM, Eichenberger P, Liu JS. Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. Journal of Multivariate Analysis. 2004 Jul;90(1 SPEC. ISS.):1-18. https://doi.org/10.1016/j.jmva.2004.02.007
Conlon, Erin M. ; Eichenberger, Patrick ; Liu, Jun S. / Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. In: Journal of Multivariate Analysis. 2004 ; Vol. 90, No. 1 SPEC. ISS. pp. 1-18.
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