Table 1

Strengths and weaknesses of the hypergeometric test and individual components of RIDDLE





Gold standard for overlapping sets

Fails for split sets

Local extension

Moderate improvement upon split sets

Diffusion - AUC

Exceptional improvement upon split sets

Considerable performance loss for GO overlap sets

Strong correlation with centrality

Diffusion - AP

Matches hypergeometric for overlapping sets

Major improvement upon split sets

Weak correlation with centrality

Strong correlation with set size


Best for split sets

Minor performance loss for GO overlap sets

AP, average precision; AUC, area under the ROC curve; GO, Gene Ontology.

Wang et al. Genome Biology 2012 13:R125   doi:10.1186/gb-2012-13-12-r125

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