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.

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

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