TABLE 4.
GO annotation based on the Biological Process ontology for temperature-regulated genes and genes differentially expressed in strainsa
| GO term | No. of ORFs | Cluster frequency (%) | P valueb |
|---|---|---|---|
| Genes downregulated at low temperatures | |||
| Response to stimulus | 166 | 21.0 | 4.53e-06 |
| Trehalose metabolic process | 9 | 1.1 | 0.00018 |
| Response to stress | 112 | 14.2 | 0.00031 |
| Biological regulation | 202 | 25.6 | 0.00618 |
| Genes upregulated at low temperatures | |||
| Ribosome biogenesis and assembly | 105 | 35.5 | 5.77e-56 |
| RNA processing | 75 | 25.3 | 1.23e-21 |
| Organelle organization and biogenesis | 120 | 40.5 | 1.00e-10 |
| Nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process | 110 | 37.2 | 1.86e-10 |
| Gene expression | 91 | 30.7 | 1.47e-07 |
| RNA modification | 15 | 5.1 | 0.00134 |
| RNA 5′ end processing | 9 | 3.0 | 0.00249 |
| Genes downregulated in the EC1118 wine strain | |||
| Sexual reproduction, conjugation | 28 | 9. | 1.41e-09 |
| Reproduction | 39 | 13.3 | 7.48e-05 |
| Transposition, RNA mediated | 7 | 2.4 | 0.00113 |
| Cytokinesis, completion of separation | 6 | 2.0 | 0.00323 |
a
No significant ontology term could be found for input genes upregulated in the EC1118 wine strain. Of 173 input genes, 52 are directly annotated to the root term “biological process unknown.”
b
The significance of overrepresentation of a cluster is expressed as a P value.