Effect of the absolute statistic on gene-sampling gene-set analysis methods

Statistical Methods in Medical Research
Dougu Nam

Abstract

Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

References

Apr 19, 2003·Genome Biology·Barry R ZeebergJohn N Weinstein
Jun 9, 2005·BMC Bioinformatics·Seon-Young Kim, David J Volsky
Sep 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Lu TianPeter J Park
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 30, 2006·Nucleic Acids Research·Vishal SaxenaIsaac Kohane
Feb 17, 2007·Bioinformatics·Jelle J Goeman, Peter Bühlmann
Jul 7, 2007·BMC Bioinformatics·Irina DinuYutaka Yasui
Oct 30, 2007·American Journal of Human Genetics·Kai WangMaja Bucan
Jan 19, 2008·Briefings in Bioinformatics·Dougu Nam, Seon-Young Kim
Feb 5, 2009·BMC Bioinformatics·Marit Ackermann, Korbinian Strimmer
Jan 6, 2010·Statistical Methods in Medical Research·Rafael A IrizarryTerence P Speed
May 27, 2010·Nucleic Acids Research·Dougu NamSangsoo Kim
Sep 9, 2010·Bioinformatics·Dougu Nam
Oct 20, 2010·BMC Genomics·Daniel M GattiFred A Wright
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
May 29, 2012·Nucleic Acids Research·Di Wu, Gordon K Smyth

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Methods Mentioned

BETA
genotyping

Software Mentioned

GSA
JAVA
MEAN
GSEA

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