Table 7.
GO biological processes assignments.
| Gene Ontology concepts | Frequency of Ontology Annotation | Brief Description | Gene Products | Coding Genes | |||
|---|---|---|---|---|---|---|---|
| Name | Frequency of Assignment | Frequency of Annotation | Name | Frequency of Annotation | |||
| GO:0008152 Metabolic process | 89% | The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. | RelA | 80% | 79% | relA | 72% |
| LacZ | 10% | 24% | lacZ | 26% | |||
| GO:0015949 Nucleobase, nucleoside and nucleotide interconversion | 80% | The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide is synthesized from another nucleobase, nucleoside or nucleotide. | RelA | 80% | 79% | relA | 72% |
| SpoT | 20% | 31% | spoT | 46% | |||
| GO:0015969 Guanosine tetraphosphate metabolic process | 80% | The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates. | RelA | 80% | 79% | relA | 72% |
| SpoT | 20% | 31% | spoT | 46% | |||
| GO:0006350 Transcription | 56% | The synthesis of either RNA on a template of DNA or DNA on a template of RNA. | RpoS | 16% | 22% | rpoS | 17% |
| CRP | 12% | 6% | crp | 4% | |||
| RpoB | 10% | 18% | rpoB | 16% | |||
| Mfd | 10% | 2% | mfd | 2% | |||
| GO:0006355 Regulation of transcription, DNA-dependent | 52% | Any process that modulates the frequency, rate or extent of DNA-dependent transcription. | RpoS | 20% | 22% | rpoS | 17% |
| CRP | 14% | 6% | crp | 4% | |||
| Mfd | 12% | 2% | mfd | 2% | |||
| GO:0006412 Translation | 40% | The cellular metabolic process by which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. | RplK | 28% | 7% | rplK | 6% |
| DksA | 28% | 8% | dksA | 3% | |||
| EF-Tu | 13% | 14% | tufB | 3% | |||
| GO:0006950 Response to stress | 39% | A change in state or activity of a cell or an organism as a result of a disturbance in cellular homeostasis, usually, but not necessarily, exogenous. | RecA | 20% | 16% | recA | 20% |
| RelB | 16% | 4% | relB | 3% | |||
| NusA | 10% | 5% | nusA | 4% | |||
| GO:0042594 Response to starvation | 39% | A change in state or activity of a cell or an organism as a result of a starvation stimulus, deprivation of nourishment. | SpoT | 67% | 31% | spoT | 46% |
| DksA | 30% | 8% | dksA | 3% | |||
| GO:0006970 Response to osmotic stress | 38% | A change in state or activity of a cell or an organism as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. | RpoS | 59% | 22% | rpoS | 17% |
| EF-Tu | 34% | 14% | tufB | 3% | |||
| GO:0005975 Carbohydrate metabolic process | 36% | The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. | LacZ | 94% | 24% | lacZ | 26% |
| GO:0006974 Response to DNA damage stimulus | 36% | A change in state or activity of a cell or an organism as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. | Mfd | 28% | 2% | mfd | 2% |
| RecA | 11% | 16% | recA | 20% | |||
| RecG | 11% | 3% | recG | NA | |||
| GO:0006281 DNA repair | 36% | The process of restoring DNA after damage that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. | Mfd | 28% | 2% | mfd | 2% |
| RecA | 11% | 16% | recA | 20% | |||
| RecG | 11% | 3% | recG | NA | |||
GO terms were assigned to annotated concepts associated with gene products annotations. A threshold of 35% of documents was considered for ontology assignment and a threshold of 10% was used to point out the gene products that most contributed to such assignment.
NA: corresponds to non-annotated genes in the corpus.