Table 4 |
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|
GO process analysis of gene targets for Cse4, Ste12 and PolII. For a complete GO analysis, please refer to Additional File 5. |
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|
GO term |
Cluster frequency |
Background frequency |
p-value |
|
|
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|
GO process categories for Cse4 |
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|
|
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|
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 |
|
|
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|
GO process categories for Ste12 |
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|
|
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|
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 |
|
|
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|
Top 40 GO process categories for PolII |
|||
|
|
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|
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. |
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|
Lefrançois et al. BMC Genomics 2009 10:37 doi:10.1186/1471-2164-10-37 |
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