TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation

Table 4 Conservation of the three [-39, -26]-PLM classes in orthologous gene pairs between A. thaliana and O. sativa.

	Number of ortholog pairs with PLM in			Percentage of PLM conservation
	A. thaliana (a)	O. sativa (b)	Both species (c)	Observed	Expected by chance:
Only TATAWA	393	343	82	17% (7e ^-15 )	6%
Only TATAΔ-PLMs	997	531	138	12% (NS)	11%
Only TC_[-39,-26]-PLMs	655	602	98	13% (NS)	12%

In the 5805 pairs of orthologous genes between A. thaliana and O. sativa, we searched for the number of genes containing a given _[-39,-26]-PLM (a) in A. thaliana but not in their respective O. sativa ortholog, (b) in O. sativa but not in their respective A. thaliana ortholog and (c) in both orthologous genes. The c/(a+c) ratio indicates the level of observed conservation for each PLM class in O. sativa in regard to A. thaliana. Then we compared the ratio to the by chance value, i.e. the ratio b/(5805-a-c): the presence of a given PLM in O. sativa orthologous genes from the PLM-less A. thaliana genes. We performed two one-sided Fisher exact tests allowing the identification of significantly different percentages. The underlined data indicate that the observed percentage is higher than expected. NS indicates non-significant difference. P-values in parenthesis are less than 5% with the Bonferroni correction.

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