Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Table 2 Structural gene features of A. thaliana genes for the four promoter classes. Gene sets Length median Percentage Gene 5’UTR CDS All introns Intron-less All genes 2293 158 1086 588 18.8 Only TATA-box 1936 (5e-23) 112 (7e-38) 966 (5e-14) 521 (1e-4) 24.5 (4e-9) Only TC[-39,-26]-PLMs 2385 (8e-8) 175 (3e-5) 1185 (3e-10) 605 (NS) 16.7 (NS) Only TATAΔ-PLMs 2293 (NS) 161 (NS) 1071 (NS) 588 (NS) 17.5 (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). Page 9 of 15 [-39,-26]-PLM-less 2334 (2e-7) 173 (9e-10) 1119 (1e-4) 614 (NS) 17.1 (NS) searched for such a link with PLMs in the [-39, -26] region using A. thaliana transcriptome data obtained with the Complete Arabidopsis Transcriptome MicroAr- ray (CATMA) [49] and available through the Complete Arabidopsis Transcriptome database: CATdb [50]. The dataset included 1044 hybridizations based on 522 dif- ferent samples covering numerous developmental stages, biotic and abiotic stresses and mutants. We used nor- malized data on which positive hybridizations have pre- viously been determined (see Methods section in Aubourg et al., [51]). For any one gene, the relative number of positive hybridizations was considered as a measure of the range of expression, i.e. of the specifi- city. To measure the global level of expression we com- puted the median of the signal intensities. The relationship between the median signal intensity and the percentage of hybridizations was clearly not linear and suggested the existence of different classes of genes with respect to transcriptional regulation. We thus clus- tered the transcriptome data into four classes (Figure 7 and Table 3, first rows). First, genes were separated in two classes depending on their expression level above or below the distribution model line, respectively HE for those with High levels of Expression and LE for those with Low levels of Expression. Second, two classes were defined relating to the specificity of hybridizations and delimited by the two inflections in the cloud of points. The first class clustered genes positively hybri- dized in less than 15% of microarray hybridizations (SR for Small Range) and the second class clustered those with more than 85% of hybridizations (WR for Wide Range). Interestingly, each of these four transcriptional clusters was predominantly made up of genes contain- ing one of a specific class of [-39,-26]-PLMs. Thus, (i) genes within the transcriptional SR group, i.e. those that hybridized in specific conditions predominantly Figure 7 Subsets of A. thaliana genes characterized by different expression intensities and specificities. Each gene is plotted according to the percentage of plant samples by which the gene specific probe has been hybridized (x-label) and to the median of expression intensities observed in the different samples (y-label). (A) First, we estimated the base line for all data (in black) and we characterized two gene groups: the highly expressed genes (HE, in magenta, 4371 genes) above the base line and the lowly expressed genes (LE, in green, 6790 genes) below the base line. Second, we identified two inflections in the base line corresponding to 15% and 85% of hybridizations (vertical dashed black lines). These limits characterized two extreme sets of genes, the genes exhibiting the Smallest Range of hybridizations (SR, 4510 genes) and the gene exhibiting the Widest Range of hybridizations (WR, 1241 genes). (B) From the SR and WR gene sets, we defined 4 sets of genes with extreme hybridization intensities by estimating an upper (magenta line) and lower (green line) bound at the 60% confidence interval. Thus, there are 618 SR-HE+, 822 SR-LE+, 244 WR-HE+ and 385 WR-LE+ genes.