Table 1. Presence of the URE3 matrix in the promoters of genes modulated by a dominant positive URE3-BP.

	Promoters which did not contain a URE3 matrix	Promoters containing a URE3 matrix 375-25 bases 5′ of ATG start codon	Total Number of Promoters analyzed	%	Statistical significance
Transcripts significantly modulated by URE3-BP	23	27	50	54	p<0.0001
All E. histolytica promoters	6527	1985	8522	23
Promoters with multiple URE3
	Promoters which did not contain at least 2 URE3 matrices
Transcripts significantly modulated by URE3-BP	40	10	50	20	p = 0.0031
All E. histolytica promoters	7862	660	8522	8
Motif Frequency in Promoters
	Nonamers not in motif	URE3 motifs	potential motifs (sequence divided by motif length 9 bp)
Transcripts significantly modulated by URE3-BP	1905	39	1944.4	2	p = 0.0025
All E. histolytica promoters	327360	4051	331411	1.2

A contingency table χ² test was used to compare the occurrence of the URE3 motif in transcripts significantly modulated by URE3 (the numbers were to large for the Fishers exact test). The motif background in all E. histolytica promoters was determined using a custom motif search script. To clearly illustrate the data we show the analysis on a promoter basis, and motif frequency per sequence nonamer.