Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Table 1 Functional category profiles of A. thaliana four gene sets. Gene sets GO Biological process GO Cellular component Response to abiotic or biotic stimulus Response to stress Protein metabolism Cell wall Ribosome Cytosol Golgi apparatus Mitochondria Plastid Chloroplast All genes 8.8 8.8 15 3.1 2.6 2.8 1.4 5.6 6.1 15 Only TATA- box 12 (7e-4) 11 (1e-3) 12 (NS) 5.8 (1e-6) 4.2 (1e-3) 5 (4e-5) 0.3 (3e-5) 3.2 (3e-5) 3.6 (6e-5) 11 (5e-6) Only TC[-39,-26]- PLMs Only TATAΔ- PLMs [-39, -26]--PLM- less 7.7 (NS) 8.6 (NS) 18 (1e-3) 1.8 (6e-4) 1.8 (NS) 1.9 (NS) 1.3 (NS) 4.8 (NS) 5.2 (NS) 15 (NS) 7.7 (NS) 8.2 (NS) 16 (NS) 3.1 (NS) 3.1 (NS) 3.2 (NS) 1.8 (NS) 6 (NS) 7 (NS) 16 (NS) Page 7 of 15 8.1 (NS) 7.7 (NS) 15 (NS) 2.7 (NS) 2.4 (NS) 2.4 (NS) 1.6 (NS) 6.6 (NS) 7 (NS) 17 (NS) Gene functional categories have been retrieved from the GO categories [60] provided by TAIR [41]. In the table, each number not in parenthesis is the percentage of genes annotated in a given GO category. We performed the two one-sided Fisher exact tests allowing the identification of enrichment (bold) or impoverishment (underlined) of GO categories in a given set of genes when compared with all the other genes, i.e. genes within the whole gene set minus genes within the considered gene set. NS indicates a non-significant difference between percentages. P-values in parenthesis are less than 5% with the Bonferroni correction. Results are only shown for GO categories exhibiting at least one bias. TFBS [42]. Here we analysed the GO annotations of the four classes of genes defined above, according to the four promoter sets. As far as biological processes are concerned, the most conspicuous observation was a pre- ferred association between genes containing a TATA- box and responses to different stimuli (Table 1, Biologi- cal Process). This result was expected since in human and in yeast the TATA-box-containing genes are more frequently involved in specific biological processes [4,9]. Interestingly, we also found that TC[-39,-26]-PLM-con- taining genes are more frequently involved in protein metabolism than any other gene class (Table 1, Biologi- cal Process), i.e. a basic biological process. Neither the TATAΔ-containing genes nor the [-39,-26]-PLM-less genes showed any significant bias for any biological pro- cess categories. We also analysed the partitioning of genes between the different GO cellular components. Again, the TATA-box-containing genes presented the most biased partitioning. The products of these genes are more often constituents of the cell wall, the cytosol and the ribosomes and less frequently constituents of the chloroplasts, the plastids, the Golgi apparatus and the mitochondria compared to the products of all the other genes (Table 1, Cellular Components). Products of the TC[-39,-26]-PLM-containing genes exhibited little biased partitioning between the GO cellular component categories. Indeed, only the cell wall component was sig- nificantly less represented. It seems biologically sound to have found a positive correlation between the response to different stimuli and the cell wall GO categories in the TATA-box-containing genes and a negative correla- tion between the protein metabolism and the cell wall categories for TC[-39,-26]-PLM-containing genes. These observations suggest that TC[-39,-26]-PLMs might have a functional role in transcriptional control that could fre- quently differ from and perhaps even oppose the TATA-box functional role. It is of particular interest that our observations support the hypothesis that small variations in the TATA-box sequence are linked to large changes in gene expression [6,43]. Unfortunately, due to the relatively small number of promoters containing a unique TC[-39,-26]-PLM, it was deemed impossible to perform the same comparisons between the TC[-39,-26]- PLM seeds alone and their predicted variants as that performed for the TA-motifs. It should be noted that by analysing all the genes containing a TC[-39,-26]-PLM alone we decreased the power of our statistical tests. We were however able to demonstrate a significant dif- ference between the TATA-box and the TC[-39,-26]-PLM sets concerning protein metabolism and cell wall cate- gories (p. values of 3e-5 and 1e-9 respectively). Only the canonical TATA-box is spatially linked to the Initiator element Recent progress in mammalian genomics has defined a more functional image of core-promoters. Two func- tional categories of core-promoters have been described [44]. The single peak promoters have a tightly defined TSS position within a few base pairs while in broad peak promoters several TSSs may be found within small clusters spanning tens of base pairs. A TATA-box is more likely to be found within single peak promoters than in broad peak promoters [44]. In genome-wide stu- dies, only the most upstream TSSs are often considered and are defined by the available transcript sequences. There are three main categories of core-promoters described in human [9], i.e. TATA-box-containing pro- moters with an Inr, TATA-box-containing promoters