Table 2

Comparison of FAIME-prioritized mechanisms against controls (standard bioinformatics)

Human Prostate Cancer Dataset

FDR

FAIME-Derived Mechanisms

Controls: Standard Bioinformatics Approaches*

Gene Ontology (n = union of {4877 up-} ∪ {4877 down-} regulated)

Cancer Module (n = {454 up-} ∪ {454 down-} regulated)

Diff. Expressed Genes

GO Enrichment from Diff. Expressed Genes (# terms; n = 4877)


Yu

0.01

28% (2703)

25% (230)

2.3% (208/8799)

0.3% (14)

0.05

32% (3137)

31% (282)

3.3% (293/8799)

0.4% (21)

Wallace

0.01

5% (441)

4% (36)

2.5% (326/12680)

0.1% (4)

0.05

13% (1226)

9% (83)

4.5% (574/12680)

0.2% (10)

Taylor

0.01

17% (1672)

12% (109)

0.7% (202/26448)

0.1% (6)

0.05

25% (2395)

19% (168)

1.0% (266/26448)

0.2% (9)


*As a comparison, differentially expressed genes (SAM, FDR ≤ 0.05) were enriched for Gene Ontology (GO) Terms using the DAVID tool. Numbers in parentheses indicate significant terms and the universe of terms from which they were drawn to generate the percentage indicated.

Chen et al. BMC Medical Genomics 2013 6(Suppl 2):S4   doi:10.1186/1755-8794-6-S2-S4

Open Data