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Table 2 Comparison of FAIME-prioritized mechanisms against controls (standard bioinformatics)

From: Curation-free biomodules mechanisms in prostate cancer predict recurrent disease

   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)
Human Prostate Cancer Dataset FDR FAIME-Derived Mechanisms Controls: Standard Bioinformatics Approaches*
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)
  1. *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.