Table 6

Ten most significant GO biological processes from the gene set enrichment analysis of the genome
GO Identifier GO Biological Process Over-Expressed Gene1 Under-Expressed Genes2 Log Odds Ratio3 FDR P-value4
GO:0046907 intracellular transport 357 560 −0.7338 3.79E-24
GO:0034613 cellular protein localization 245 433 −0.8490 4.78E-24
GO:0043067 regulation of programmed cell death  351 490 −0.6110 1.68E-15
GO:0016192 vesicle-mediated transport 271 400 −0.6639 1.16E-14
GO:0006629 lipid metabolic process 424 538 −0.5148 1.30E-12
GO:0044265 cellular macromolecule catabolic process  373 485 −0.5379 2.10E-12
GO:0044255 cellular lipid metabolic process 346 457 −0.5528 2.41E-12
GO:0050793 regulation of developmental process  442 549 −0.4932 4.27E-12
GO:0007049 cell cycle 418 522 −0.4978 1.11E-11
GO:0009966 regulation of signal transduction 414 509 −0.4812 9.93E-11

1Over-Expressed Genes: number of genes that have a positive association between expression and glioblastoma multiforme survival.

2Under-Expressed Genes: number of genes that have a negative association between expression and glioblastoma multiforme survival.

3Log Odds Ratio: indicates whether the category is more enriched among the genes that have a positive association between expression and survival relative to the enrichment among the genes that have a negative association between expression and glioblastoma survival (positive loge odds ratio) or vice versa (negative loge odds ratio). Extreme values indicate higher difference in the enrichment percentages between the positive and negative association groups meanwhile values close to zero indicate similar enrichment percentages between positive and negative association groups.

4FDR-adjusted P-value: False discovery rate adjusted P-value of the log odds ratio test.

Sadeque et al.

Sadeque et al. BMC Medical Genomics 2012 5:59   doi:10.1186/1755-8794-5-59

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