A Bayesian variable selection procedure to rank overlapping gene sets.

BMC Bioinformatics
Axel SkarmanPeter Sørensen

Abstract

Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prioritize gene sets, such as the genes in a given molecular pathway, have been described. In many cases, these methods test one gene set at a time, and therefore do not consider overlaps among the pathways. Here, we present a Bayesian variable selection method to prioritize gene sets that overcomes this limitation by considering all gene sets simultaneously. We applied Bayesian variable selection to differential expression to prioritize the molecular and genetic pathways involved in the responses to Escherichia coli infection in Danish Holstein cows. We used a Bayesian variable selection method to prioritize Kyoto Encyclopedia of Genes and Genomes pathways. We used our data to study how the variable selection method was affected by overlaps among the pathways. In addition, we compared our approach to another that ignores the overlaps, and studied the differences in the prioritization. The variable selection method was robust to a change in prior probability and stable given a limited number of observations. Bayesian variable s...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Nov 28, 2006·Bioinformatics·Zhen Jiang, Robert Gentleman
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Roberto R Ricardo-GonzalezAjay Chawla

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Methods Mentioned

BETA
biopsies

Software Mentioned

GSEA
Bioconductor
Bt
org
Gene Set Enrichment Analysis ( GSEA )
R package Limma
. db
Affy package
TopGO
iBay

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