Table 4 GO process analysis of gene targets for Cse4, Ste12 and PolII. For a complete GO analysis, please refer to Additional File 5.
From: Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
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 |