Table 2

Structural gene features 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


Length median

Gene

2293

    1936 (5e-23)

2385 (8e-8)

2293 (NS)

2334 (2e-7)

5'UTR

158

    112 (7e-38)

175 (3e-5)

161 (NS)

173 (9e-10)

CDS

1086

    966 (5e-14)

1185 (3e-10)

1071 (NS)

1119 (1e-4)

All introns

588

    521 (1e-4)

605 (NS)

588 (NS)

614 (NS)


Percentage

Intron-less

18.8

24.5 (4e-9)

16.7 (NS)

17.5 (NS)

17.1 (NS)


Structural gene features have been assigned by querying the FLAGdb++ database [59]. For median length data, we performed two one-sided Wilcoxon tests allowing the identification of enrichment in wide (bold) or in compact gene structures (underlined) in a set of genes compared with all the other genes, i.e. genes within the whole gene set minus genes within the considered gene set. For intron-less gene percentages, 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 the other genes. NS indicates a non-significant difference. P-values in parenthesis are less than 5% with the Bonferroni correction. Both the first intron and 3'UTR lengths are never biased (data not shown).

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

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