Table 2

Summary of GO analysis for D- and S-pair duplicates

D-pair
 S-pair




Biological process*
 No.
 Percentage
 No.
 Percentage
 P-value†
 Excess‡
Biosynthetic process
 32
 21.1
 111
 42.9
 0.0008
 56
Catabolic process
 32
 21.1
 17
 6.6
 0.0024
 22
Regulation of biological process
 59
 38.8
 56
 21.6
 0.0172
 26
Response to biotic stimulus
 0
 0.0
 12
 4.6
 0.1480
 12
Nitrogen compound metabolic process
 4
 2.6
 21
 8.1
 0.3988
 14
Cell communication
 18
 11.8
 15
 5.8
 0.4587
 9
Primary metabolic process
 110
 72.4
 210
 81.1
 0.5012
 23
Cell cycle
 21
 13.8
 20
 7.7
 0.5012
 9
Response to endogenous stimulus
 12
 7.9
 9
 3.5
 0.5012
 7
Chemical homeostasis
 0
 0.0
 6
 2.3
 0.5012
 6
Cellular developmental process
 11
 7.2
 9
 3.5
 0.5012
 6
Chromosome segregation
 5
 3.3
 2
 0.8
 0.5012
 4
Cell division
 21
 13.8
 25
 9.7
 0.6028
 6
Response to stress
 24
 15.8
 29
 11.2
 0.6483
 7
Reproductive process
 14
 9.2
 15
 5.8
 0.6696
 5
Conjugation
 7
 4.6
 6
 2.3
 0.6982
 3
Sexual reproduction
 7
 4.6
 6
 2.3
 0.6982
 3
Aging
 1
 0.7
 6
 2.3
 0.7084
 4
Cellular metabolic process
 120
 79.0
 214
 82.6
 0.7686
 9
Asexual reproduction
 3
 2.0
 2
 0.8
 0.7686
 2
Nuclear division
 1
 0.7
 0
 0.0
 0.7686
 1
Protein localization
 10
 6.6
 23
 8.9
 0.7785
 6
Cell adhesion
 0
 0.0
 2
 0.8
 0.7785
 2
Response to chemical stimulus
 17
 11.2
 25
 9.7
 0.8583
 2
RNA localization
 6
 4.0
 9
 3.5
 0.9959
 1
Anatomical structure development
 12
 7.9
 19
 7.3
 1
 1
Establishment of localization
 33
 21.7
 55
 21.2
 1
 1
Macromolecule metabolic process
 98
 64.5
 169
 65.3
 1
 2
Response to external stimulus
 0
 0.0
 1
 0.4
 1
 1
Maintenance of localization
 1
 0.7
 1
 0.4
 1
 0
Response to abiotic stimulus
 4
 2.6
 7
 2.7
 1
 0
Cell organization and biogenesis
 57
 37.5
 97
 37.5
 1
 0
Regulation of biological quality
 8
 5.3
 14
 5.4
 1
 0
Autophagy
 0
 0.0
 1
 0.4
 1
 1
Filamentous growth
 8
 5.3
 13
 5.0
 1
 0
Cell homeostasis
 7
 4.6
 12
 4.6
 1
 0
Regulation of a molecular function
 1
 0.7
 3
 1.2
 1
 1
Cell proliferation
 0
 0.0
 1
 0.4
 1
 1
Non-developmental growth
 1
 0.7
 2
 0.8
 1
 0

*We selected GO level 3, since this constitutes a good compromise between the number of genes annotated and the depth of the information contained in each class [46]. †After false discovery rate correction. ‡Represents the difference between the observed number of genes in the over-represented set and what would be expecated based on the observed genes in the other gene set.

Marques et al. Genome Biology 2008 9:R54   doi:10.1186/gb-2008-9-3-r54