TABLE 1 .

Enrichment of the URE3 consensus motif in transcripts changed 2-fold in vivo^a

Parameter	No. of promoters containing a URE3 matrix 375 to 25 bases 5′ of ATG start	No. of promoters without a URE3 matrix	Total no. (%) of promoters analyzed	P value
No. of promoters of transcripts modulated in luminal amebae	54	85	139 (39)	<0.0001
No. of promoters of unchanged E. histolytica transcripts	1,931	6,452	8,383 (23)
Total no. (%) of promoters analyzed	1,985 (2.7)	6,537 (1.3)	8,522 (100)

^aA contingency table χ² test was used to compare the occurrences of the URE3 motif in transcripts significantly modulated by at least 2-fold at day 1 in vivo. These were identified by the use of the Linear Model for Microarray Data, and the false-discovery rate was corrected by the use of the Benjamini and Hochberg equation as described in Materials and Methods. Promoters were defined as the region from −375 bp to −25 bp 5′ of the initiating ATG of the structural gene. Background motif levels in E. histolytica promoters were determined as previously described (6).