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Multiple testing for gene sets from microarray experiments.

Publication ,  Journal Article
Sohn, I; Owzar, K; Lim, J; George, SL; Mackey Cushman, S; Jung, S-H
Published in: BMC Bioinformatics
May 26, 2011

BACKGROUND: A key objective in many microarray association studies is the identification of individual genes associated with clinical outcome. It is often of additional interest to identify sets of genes, known a priori to have similar biologic function, associated with the outcome. RESULTS: In this paper, we propose a general permutation-based framework for gene set testing that controls the false discovery rate (FDR) while accounting for the dependency among the genes within and across each gene set. The application of the proposed method is demonstrated using three public microarray data sets. The performance of our proposed method is contrasted to two other existing Gene Set Enrichment Analysis (GSEA) and Gene Set Analysis (GSA) methods. CONCLUSIONS: Our simulations show that the proposed method controls the FDR at the desired level. Through simulations and case studies, we observe that our method performs better than GSEA and GSA, especially when the number of prognostic gene sets is large.

Duke Scholars

Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

May 26, 2011

Volume

12

Start / End Page

209

Location

England

Related Subject Headings

  • Oligonucleotide Array Sequence Analysis
  • Lung Neoplasms
  • Humans
  • Genetic Association Studies
  • Gene Expression Profiling
  • Bioinformatics
  • 49 Mathematical sciences
  • 46 Information and computing sciences
  • 31 Biological sciences
  • 08 Information and Computing Sciences
 

Citation

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Sohn, I., Owzar, K., Lim, J., George, S. L., Mackey Cushman, S., & Jung, S.-H. (2011). Multiple testing for gene sets from microarray experiments. BMC Bioinformatics, 12, 209. https://doi.org/10.1186/1471-2105-12-209
Sohn, Insuk, Kouros Owzar, Johan Lim, Stephen L. George, Stephanie Mackey Cushman, and Sin-Ho Jung. “Multiple testing for gene sets from microarray experiments.BMC Bioinformatics 12 (May 26, 2011): 209. https://doi.org/10.1186/1471-2105-12-209.
Sohn I, Owzar K, Lim J, George SL, Mackey Cushman S, Jung S-H. Multiple testing for gene sets from microarray experiments. BMC Bioinformatics. 2011 May 26;12:209.
Sohn, Insuk, et al. “Multiple testing for gene sets from microarray experiments.BMC Bioinformatics, vol. 12, May 2011, p. 209. Pubmed, doi:10.1186/1471-2105-12-209.
Sohn I, Owzar K, Lim J, George SL, Mackey Cushman S, Jung S-H. Multiple testing for gene sets from microarray experiments. BMC Bioinformatics. 2011 May 26;12:209.
Journal cover image

Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

May 26, 2011

Volume

12

Start / End Page

209

Location

England

Related Subject Headings

  • Oligonucleotide Array Sequence Analysis
  • Lung Neoplasms
  • Humans
  • Genetic Association Studies
  • Gene Expression Profiling
  • Bioinformatics
  • 49 Mathematical sciences
  • 46 Information and computing sciences
  • 31 Biological sciences
  • 08 Information and Computing Sciences