Table 3

Evaluation of the overlap among different approaches to prioritize classifier's mechanisms

Approaches to Prioritize Classifier's Mechanisms

Overlapping Mechanism (#)

% of each compared set

Overlapping p-value (FET)


FAIME-Derived Approaches

Overlap-Gene Ontology

Yu ∩ Wallace

462

15%; 38%

6.9 x10-6

Yu ∩ Taylor

824

26%;34%

3.8 x10-3

Wallace ∩ Taylor

360

29%;15%

2.2 x10-5

Yu ∩ Wallace ∩ Taylor

137

4%;11%;6%

Overlap Cancer Module

Yu ∩ Wallace

41

15%;49%

1.9x10-4

Yu ∩ Taylor

77

27%;46%

5.7 x10-6

Wallace ∩ Taylor

25

30%;15%

4.8 x10-4

Yu ∩ Wallace ∩ Taylor

14

5%;17%;8%


Controls: Standard Bioinformatics Approaches

Overlap of Differentially Expressed Genes

Yu ∩ Wallace

33

11%;6%

6.1 x10-9

Yu ∩ Taylor

65

22%;24%

<2 x10-16

Wallace ∩ Taylor

20

3%;8%

1.5 x10-3

Yu ∩ Wallace ∩ Taylor

7

2%;1%;3%

Overlap GO derived from Differentially Expressed Genes

Yu ∩ Wallace

1

5%;10%

4.2 x10-2

Yu ∩ Taylor

0

NA

NS

Wallace ∩ Taylor

0

NA

NS

Yu ∩ Wallace ∩ Taylor

0

NA

NS


Legend: NA = not applicable; NS = not significant; #= count of significant mechanisms overlap

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

Open Data