Skip to main content

Table 3 Performance comparison of five module inference tools

From: Identifying gene regulatory modules of heat shock response in yeast

Algorithm name TP FP FN Jaccard similarity score
HIMIA 7 5 25 0.19
ReMoDiscoery 11 38 21 0.16
GRAM 13 56 19 0.15
MOFA 8 32 24 0.13
SAMBA 10 54 22 0.12
  1. Performance comparison was based on the Jaccard similarity score [12, 34], which scores the overlap between an algorithm's output and the list of known stress-responsive TFs. Specifically, the score is defined as TP/(TP+FP+FN) [12, 34], where TP stands for true positives, FP for false positives, and FN for false negatives. Note that the higher the Jaccard similarity score, the better the ability of an algorithm to retrieve the known stress-responsive TFs.