Table 1

Specific MEA methods tested in this study.

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

PASTAA

AMA-like

1/p

X, YCPM

Spearman

AMA

1/p

none

LR

RMA

-log(p)

none

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.

McLeay and Bailey BMC Bioinformatics 2010 11:165   doi:10.1186/1471-2105-11-165