TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation

Table 1 Functional category profiles of A. thaliana four gene sets.

Gene sets		All genes	Only TATA-box	Only TC_[-39,-26]-PLMs	Only TATAΔ-PLMs	[-39, -26]^--PLM-less
GO Biological process	Response to abiotic or biotic stimulus	8.8	12 (7e ^-4 )	7.7 (NS)	7.7 (NS)	8.1 (NS)
	Response to stress	8.8	11 (1e ^-3 )	8.6 (NS)	8.2 (NS)	7.7 (NS)
	Protein metabolism	15	12 (NS)	18 (1e ^-3 )	16 (NS)	15 (NS)
GO Cellular component	Cell wall	3.1	5.8 (1e ^-6 )	1.8 (6e ^-4 )	3.1 (NS)	2.7 (NS)
	Ribosome	2.6	4.2 (1e ^-3 )	1.8 (NS)	3.1 (NS)	2.4 (NS)
	Cytosol	2.8	5 (4e ^-5 )	1.9 (NS)	3.2 (NS)	2.4 (NS)
	Golgi apparatus	1.4	0.3 (3e ^-5 )	1.3 (NS)	1.8 (NS)	1.6 (NS)
	Mitochondria	5.6	3.2 (3e ^-5 )	4.8 (NS)	6 (NS)	6.6 (NS)
	Plastid	6.1	3.6 (6e ^-5 )	5.2 (NS)	7 (NS)	7 (NS)
	Chloroplast	15	11 (5e ^-6 )	15 (NS)	16 (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.

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