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Table 1 Specific MEA methods tested in this study.

From: Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

Method Name Motif Affinity Function (X g ) Biological Signal (Y g ) Partition Maximization Variants
Fisher MC: {0, 1} 1/p YFP, YCPM, YUPM
mHG MC: {0, 1, 2} 1/p YFP, YCPM, YUPM
Ranksum AMA 1/p YFP, YCPM, YUPM
Clover AMA 1/p YFP, YCPM, YUPM
Spearman AMA 1/p none
LR RMA -log(p) none
  1. The method names refer to the association function they use: "Fisher" (Fisher Exact Test), "mHG" (multi-hypergeometric test), "Ranksum" (Ranksum or Mann-Whitney U Test), "Clover", "Spearman" (Spearman's rank correlation coefficient) and "LR" (linear regression). For Fisher, the MC motif affinity function is capped at 1 match; for mHG, the MC function is capped at 2 matches. We set t m = 0.0002 for the MC motif affinity function (i.e., matches have PWM score with p-value less than 0.0002). In all methods except LR, Y g is defined as 1/p, where p is the p-value of a microarray probe fluorescence signal; for the LR method, Y g is defined as p.