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Table 1 Strengths and weaknesses of the hypergeometric test and individual components of RIDDLE

From: RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network

Method

Strengths

Weaknesses

Hypergeometric

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

RIDDLE

Best for split sets

Minor performance loss for GO overlap sets

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