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.

Bernard et al. BMC Genomics 2010 11:166   doi:10.1186/1471-2164-11-166

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