Skip to main content

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.