Table 4

GO process analysis of gene targets for Cse4, Ste12 and PolII. For a complete GO analysis, please refer to Additional File 5.

GO term

Cluster frequency

Background frequency

p-value


GO process categories for Cse4


glycolysis

8 out of 132 genes, 6.1%

22 out of 7158 background genes, 0.3%

8.32e-07

glucose catabolic process

8 out of 132 genes, 6.1%

32 out of 7158 background genes, 0.4%

2.34e-05

alcohol metabolic process

16 out of 132 genes, 12.1%

179 out of 7158 background genes, 2.5%

4.49e-05

hexose catabolic process

8 out of 132 genes, 6.1%

37 out of 7158 background genes, 0.5%

7.96e-05

cellular biosynthetic process

57 out of 132 genes, 43.2%

1689 out of 7158 background genes, 23.6%

0.00013

monosaccharide catabolic process

8 out of 132 genes, 6.1%

42 out of 7158 background genes, 0.6%

0.00023

alcohol catabolic process

8 out of 132 genes, 6.1%

45 out of 7158 background genes, 0.6%

0.00039

pyruvate metabolic process

7 out of 132 genes, 5.3%

39 out of 7158 background genes, 0.5%

0.00174

hexose metabolic process

9 out of 132 genes, 6.8%

78 out of 7158 background genes, 1.1%

0.00349

biosynthetic process

58 out of 132 genes, 43.9%

1929 out of 7158 background genes, 26.9%

0.00496

hexose biosynthetic process

6 out of 132 genes, 4.5%

31 out of 7158 background genes, 0.4%

0.00529

glucose metabolic process

8 out of 132 genes, 6.1%

64 out of 7158 background genes, 0.9%

0.00601


GO process categories for Ste12


biological regulation

193 out of 823 genes, 23.5%

1132 out of 7158 background genes, 15.8%

7.46e-07

regulation of cellular process

158 out of 823 genes, 19.2%

889 out of 7158 background genes, 12.4%

2.02e-06

regulation of biological process

160 out of 823 genes, 19.4%

904 out of 7158 background genes, 12.6%

2.13e-06

monosaccharide transport

15 out of 823 genes, 1.8%

24 out of 7158 background genes, 0.3%

3.48e-06

hexose transport

15 out of 823 genes, 1.8%

24 out of 7158 background genes, 0.3%

3.48e-06

multi-organism process

40 out of 823 genes, 4.9%

136 out of 7158 background genes, 1.9%

9.27e-06

response to pheromone

32 out of 823 genes, 3.9%

96 out of 7158 background genes, 1.3%

1.03e-05

response to chemical stimulus

86 out of 823 genes, 10.4%

412 out of 7158 background genes, 5.8%

1.18e-05

response to stimulus

144 out of 823 genes, 17.5%

818 out of 7158 background genes, 11.4%

2.41e-05

cellular carbohydrate metabolic process

47 out of 823 genes, 5.7%

187 out of 7158 background genes, 2.6%

0.00011

growth

40 out of 823 genes, 4.9%

148 out of 7158 background genes, 2.1%

0.00012

regulation of transcription from RNA Pol II

56 out of 823 genes, 6.8%

243 out of 7158 background genes, 3.4%

0.00017

regulation of cell size

34 out of 823 genes, 4.1%

117 out of 7158 background genes, 1.6%

0.00017

sexual reproduction

34 out of 823 genes, 4.1%

120 out of 7158 background genes, 1.7%

0.00033

conjugation

34 out of 823 genes, 4.1%

120 out of 7158 background genes, 1.7%

0.00033

conjugation with cellular fusion

34 out of 823 genes, 4.1%

120 out of 7158 background genes, 1.7%

0.00033

response to abiotic stimulus

32 out of 823 genes, 3.9%

111 out of 7158 background genes, 1.6%

0.00047

cellular structure morphogenesis

40 out of 823 genes, 4.9%

156 out of 7158 background genes, 2.2%

0.00057

anatomical structure development

40 out of 823 genes, 4.9%

156 out of 7158 background genes, 2.2%

0.00057

cell morphogenesis

40 out of 823 genes, 4.9%

156 out of 7158 background genes, 2.2%

0.00057

anatomical structure morphogenesis

40 out of 823 genes, 4.9%

156 out of 7158 background genes, 2.2%

0.00057

signal transduction

51 out of 823 genes, 6.2%

222 out of 7158 background genes, 3.1%

0.00067

carbohydrate metabolic process

49 out of 823 genes, 6.0%

210 out of 7158 background genes, 2.9%

0.00068

external encapsulating structure organization

48 out of 823 genes, 5.8%

206 out of 7158 background genes, 2.9%

0.00093

cell wall organization and biogenesis

48 out of 823 genes, 5.8%

206 out of 7158 background genes, 2.9%

0.00093

carboxylic acid metabolic process

67 out of 823 genes, 8.1%

332 out of 7158 background genes, 4.6%

0.00195

organic acid metabolic process

67 out of 823 genes, 8.1%

332 out of 7158 background genes, 4.6%

0.00195

carbohydrate transport

15 out of 823 genes, 1.8%

35 out of 7158 background genes, 0.5%

0.00254

cell growth

26 out of 823 genes, 3.2%

87 out of 7158 background genes, 1.2%

0.00268

reproduction

65 out of 823 genes, 7.9%

323 out of 7158 background genes, 4.5%

0.00309

hexose metabolic process

24 out of 823 genes, 2.9%

78 out of 7158 background genes, 1.1%

0.00367

glucose metabolic process

21 out of 823 genes, 2.6%

64 out of 7158 background genes, 0.9%

0.00478

pseudohyphal growth

21 out of 823 genes, 2.6%

65 out of 7158 background genes, 0.9%

0.00631

cell communication

56 out of 823 genes, 6.8%

271 out of 7158 background genes, 3.8%

0.00665

nitrogen compound metabolic process

51 out of 823 genes, 6.2%

241 out of 7158 background genes, 3.4%

0.00860

establishment and maintenance of cell polarity

32 out of 823 genes, 3.9%

126 out of 7158 background genes, 1.8%

0.00953


Top 40 GO process categories for PolII


cellular process

1864 out of 2508 genes, 74.3%

4710 out of 7158 background genes, 65.8%

8.82e-27

ribonucleoprotein complex biogenesis

289 out of 2508 genes, 11.5%

494 out of 7158 background genes, 6.9%

3.36e-25

ribosome biogenesis

246 out of 2508 genes, 9.8%

407 out of 7158 background genes, 5.7%

7.01e-24

cellular component organization and biogenesis

785 out of 2508 genes, 31.3%

1725 out of 7158 background genes, 24.1%

4.02e-22

organelle organization and biogenesis

621 out of 2508 genes, 24.8%

1331 out of 7158 background genes, 18.6%

2.59e-19

primary metabolic process

1276 out of 2508 genes, 50.9%

3187 out of 7158 background genes, 44.5%

1.59e-12

maturation of SSU-rRNA from tricistronic rRNA

49 out of 2508 genes, 2.0%

60 out of 7158 background genes, 0.8%

1.86e-10

RNA metabolic process

486 out of 2508 genes, 19.4%

1082 out of 7158 background genes, 15.1%

2.71e-10

nucleotide and nucleic acid metabolic process

649 out of 2508 genes, 25.9%

1512 out of 7158 background genes, 21.1%

6.60e-10

maturation of SSU-rRNA

49 out of 2508 genes, 2.0%

62 out of 7158 background genes, 0.9%

1.97e-09

rRNA metabolic process

143 out of 2508 genes, 5.7%

257 out of 7158 background genes, 3.6%

7.39e-09

ribosomal large subunit biogenesis

50 out of 2508 genes, 2.0%

65 out of 7158 background genes, 0.9%

7.46e-09

ribonucleoprotein complex assembly

96 out of 2508 genes, 3.8%

156 out of 7158 background genes, 2.2%

1.23e-08

macromolecule metabolic process

1096 out of 2508 genes, 43.7%

2752 out of 7158 background genes, 38.4%

1.71e-08

biopolymer metabolic process

1033 out of 2508 genes, 41.2%

2580 out of 7158 background genes, 36.0%

2.55e-08

ribosomal subunit assembly

44 out of 2508 genes, 1.8%

56 out of 7158 background genes, 0.8%

4.08e-08

cellular localization

303 out of 2508 genes, 12.1%

644 out of 7158 background genes, 9.0%

4.38e-08

ribosome assembly

49 out of 2508 genes, 2.0%

65 out of 7158 background genes, 0.9%

4.46e-08

cellular metabolic process

1340 out of 2508 genes, 53.4%

3448 out of 7158 background genes, 48.2%

4.55e-08

metabolic process

1356 out of 2508 genes, 54.1%

3496 out of 7158 background genes, 48.8%

6.00e-08

rRNA processing

137 out of 2508 genes, 5.5%

250 out of 7158 background genes, 3.5%

9.13e-08

ncRNA processing

172 out of 2508 genes, 6.9%

335 out of 7158 background genes, 4.7%

3.92e-07

cellular macromolecular complex organization

184 out of 2508 genes, 7.3%

364 out of 7158 background genes, 5.1%

4.79e-07

establishment of localization in cell

278 out of 2508 genes, 11.1%

594 out of 7158 background genes, 8.3%

6.51e-07

RNA processing

234 out of 2508 genes, 9.3%

487 out of 7158 background genes, 6.8%

9.22e-07

gene expression

704 out of 2508 genes, 28.1%

1708 out of 7158 background genes, 23.9%

9.27e-07

intracellular transport

260 out of 2508 genes, 10.4%

551 out of 7158 background genes, 7.7%

9.36e-07

regulation of translation

38 out of 2508 genes, 1.5%

49 out of 7158 background genes, 0.7%

1.88e-06

maturation of 5.8S rRNA

37 out of 2508 genes, 1.5%

48 out of 7158 background genes, 0.7%

4.22e-06

maturation of 5.8S rRNA from tricistronic rRNA

37 out of 2508 genes, 1.5%

48 out of 7158 background genes, 0.7%

4.22e-06

posttranscriptional regulation of gene expression

44 out of 2508 genes, 1.8%

61 out of 7158 background genes, 0.9%

4.99e-06

macromolecular complex subunit organization

197 out of 2508 genes, 7.9%

404 out of 7158 background genes, 5.6%

5.30e-06

nuclear export

64 out of 2508 genes, 2.6%

102 out of 7158 background genes, 1.4%

1.28e-05

localization

448 out of 2508 genes, 17.9%

1046 out of 7158 background genes, 14.6%

1.35e-05

nuclear transport

76 out of 2508 genes, 3.0%

128 out of 7158 background genes, 1.8%

1.86e-05

nucleocytoplasmic transport

76 out of 2508 genes, 3.0%

128 out of 7158 background genes, 1.8%

1.86e-05

cleavages during rRNA processing

29 out of 2508 genes, 1.2%

36 out of 7158 background genes, 0.5%

3.89e-05

RNA 5'-end processing

26 out of 2508 genes, 1.0%

31 out of 7158 background genes, 0.4%

4.30e-05

transcription from RNA polymerase I promoter

30 out of 2508 genes, 1.2%

38 out of 7158 background genes, 0.5%

5.25e-05

regulation of cellular biosynthetic process

46 out of 2508 genes, 1.8%

68 out of 7158 background genes, 0.9%

5.66e-05


GO process analysis (p < 0.01) for Cse4 combined targets, for Ste12 combined targets and for PolII combined targets.

For a complete GO analysis, please refer to Additional File 5.

Lefran├žois et al. BMC Genomics 2009 10:37   doi:10.1186/1471-2164-10-37

Open Data