Table 3

Expression of A. thaliana genes for the four promoter classes.

Gene sets

All genes

Only TATA-box

Only TC[-39,-26]-PLMs

Only TATAΔ-PLMs

[-39,-26]-PLM-less


HE

39.2%

53.8% (< 1e-30)

36.7% (NS)

38.1% (NS)

    34.5% (1e-22)

LE

60.8%

    46.2% (2e-24)

63.3% (NS)

61.9% (NS)

65.5% (< 1e-30)

SR

40.4%

41% (NS)

44.1% (< 1e-30)

    37.4% (< 1e-30)

40.2% (NS)

WR

11.1%

10.3% (NS)

9.3% (NS)

13.2% (< 1e-30)

11.2% (NS)


WR-HE+

2.2%

2.4% (NS)

1.6% (NS)

2.2% (NS)

2.3% (NS)

WR-LE+

3.4%

2.5% (NS)

3.1% (NS)

4.0% (NS)

3.8% (NS)

SR-HE+

5.5%

8.5% (1e-5)

5.3% (NS)

5.3% (NS)

    4.6% (8e-6)

SR-LE+

7.4%

    5% (< 1e-30)

8.6% (NS)

6.8% (NS)

8.1% (< 1e-30)


The 8 expression categories are described in the Figure 7. HE, High Expression; LE, Low Expression; SR Small Range of expression; WR, Wide Range of expression; HE+ Highest Expressions; LE+, Lowest Expressions. The whole gene set contains the 11161 genes for which we have both a known TSS and CATMA-expression data. We performed two one-sided Fisher exact tests allowing the identification of higher (bold) or lower (underlined) percentages in a gene set in comparison with all other genes, i.e. genes within the whole gene set minus genes within the considered gene set. 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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