Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets

BMC Genomics

Table 1 A comparison based on two data sets.

Gene sets enriched in poor outcome	FDR
Boston data
Hypoxia and p53 in the cardiovascular system	<0.001
Aminoacyl tRNA biosynthesis	<0.001
Insulin upregulated genes	<0.001
tRNA synthetases	<0.001
Leucine deprivation down-regulated genes	<0.001
Telomerase up-regulated genes	<0.001
Glutamine deprivation down-regulated genes	<0.001
Cell cycle checkpoint	<0.001
Michigan data
Glycolysis gluconeogenesis	<0.001
vegf pathway	<0.001
Insulin up-regulated genes	<0.001
Insulin signaling	0.021
Telomerase up-regulated genes	<0.001
Glutamate metabolism	0.018
Ceramide pathway	0.076
p53 signalling	<0.001
tRNA synthetases	<0.001
Breast cancer estrogen signalling	<0.001
Aminoacyl tRNA biosynthesis	<0.001

Gene sets identified by Subramanian, Tamayo et al. [8] for Boston and Michigan data are listed with the false discovery rates (FDRs) calculated by our proposed concordant integrative gene set enrichment analysis. Based on the gene set enrichment analysis (GSEA) for each individual data set, the FDRs calculated by Subramanian, Tamayo et al. [8] were between 0.006 to 0.25 (most of them were between 0.1 to 0.2).

ISSN: 1471-2164